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Kon K, Ode KL, Mano T, Fujishima H, Takahashi RR, Tone D, Shimizu C, Shiono S, Yada S, Matsuzawa K, Yoshida SY, Yoshida Garçon J, Kaneko M, Shinohara Y, Yamada RG, Shi S, Miyamichi K, Sumiyama K, Kiyonari H, Susaki EA, Ueda HR. Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation. Nat Commun 2024; 15:6054. [PMID: 39025867 PMCID: PMC11258272 DOI: 10.1038/s41467-024-50168-5] [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: 03/27/2023] [Accepted: 07/01/2024] [Indexed: 07/20/2024] Open
Abstract
The homeostatic regulation of sleep is characterized by rebound sleep after prolonged wakefulness, but the molecular and cellular mechanisms underlying this regulation are still unknown. In this study, we show that Ca2+/calmodulin-dependent protein kinase II (CaMKII)-dependent activity control of parvalbumin (PV)-expressing cortical neurons is involved in homeostatic regulation of sleep in male mice. Prolonged wakefulness enhances cortical PV-neuron activity. Chemogenetic suppression or activation of cortical PV neurons inhibits or induces rebound sleep, implying that rebound sleep is dependent on increased activity of cortical PV neurons. Furthermore, we discovered that CaMKII kinase activity boosts the activity of cortical PV neurons, and that kinase activity is important for homeostatic sleep rebound. Here, we propose that CaMKII-dependent PV-neuron activity represents negative feedback inhibition of cortical neural excitability, which serves as the distributive cortical circuits for sleep homeostatic regulation.
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Affiliation(s)
- Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Kennedy Krieger Institute, Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Tomoyuki Mano
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Computational Neuroethology Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan
| | - Riina R Takahashi
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Daisuke Tone
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Shinnosuke Shiono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Saori Yada
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kyoko Matsuzawa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Shota Y Yoshida
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
| | - Junko Yoshida Garçon
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Yuta Shinohara
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan
| | - Shoi Shi
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazunari Miyamichi
- Laboratory for Comparative Connectomics, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research (BDR), Chuou-ku, Kobe, Hyogo, Japan
| | - Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, Japan.
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Department of Systems Biology, Institute of Life Science, Kurume University, Kurume, Fukuoka, Japan.
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2
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Nakamura K, Aoyama-Ishiwatari S, Nagao T, Paaran M, Obara CJ, Sakurai-Saito Y, Johnston J, Du Y, Suga S, Tsuboi M, Nakakido M, Tsumoto K, Kishi Y, Gotoh Y, Kwak C, Rhee HW, Seo JK, Kosako H, Potter C, Carragher B, Lippincott-Schwartz J, Polleux F, Hirabayashi Y. PDZD8-FKBP8 tethering complex at ER-mitochondria contact sites regulates mitochondrial complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554218. [PMID: 38895210 PMCID: PMC11185567 DOI: 10.1101/2023.08.22.554218] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identified the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-Electron Microscopy (Cryo-EM) tomography, and correlative light-EM (CLEM). Single molecule tracking revealed highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and capture at MERCS. Overexpression of FKBP8 was sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrated their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.
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3
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Arnold KA, Moran MC, Shi H, van Vlijmen-Willems IMJJ, Rodijk-Olthuis D, Smits JPH, Brewer MG. CLDN1 knock out keratinocytes as a model to investigate multiple skin disorders. Exp Dermatol 2024; 33:e15084. [PMID: 38711223 DOI: 10.1111/exd.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 05/08/2024]
Abstract
The transmembrane protein claudin-1 is critical for formation of the epidermal barrier structure called tight junctions (TJ) and has been shown to be important in multiple disease states. These include neonatal ichthyosis and sclerosing cholangitis syndrome, atopic dermatitis and various viral infections. To develop a model to investigate the role of claudin-1 in different disease settings, we used CRISPR/Cas9 to generate human immortalized keratinocyte (KC) lines lacking claudin-1 (CLDN1 KO). We then determined whether loss of claudin-1 expression affects epidermal barrier formation/function and KC differentiation/stratification. The absence of claudin-1 resulted in significantly reduced barrier function in both monolayer and organotypic cultures. CLDN1 KO cells demonstrated decreases in gene transcripts encoding the barrier protein filaggrin and the differentiation marker cytokeratin-10. Marked morphological differences were also observed in CLDN1 KO organotypic cultures including diminished stratification and reduced formation of the stratum granulosum. We also detected increased proliferative KC in the basale layer of CLDN1 KO organotypic cultures. These results further support the role of claudin-1 in epidermal barrier and suggest an additional role of this protein in appropriate stratification of the epidermis.
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Affiliation(s)
- Kimberly A Arnold
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Mary C Moran
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Huishan Shi
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Ivonne M J J van Vlijmen-Willems
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
| | - Diana Rodijk-Olthuis
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
| | - Jos P H Smits
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
- Department of Dermatology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Matthew G Brewer
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA
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4
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Xing L, Zou X, Yin C, Webb JM, Shi G, Ptáček LJ, Fu YH. Diverse roles of pontine NPS-expressing neurons in sleep regulation. Proc Natl Acad Sci U S A 2024; 121:e2320276121. [PMID: 38381789 PMCID: PMC10907243 DOI: 10.1073/pnas.2320276121] [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: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Neuropeptide S (NPS) was postulated to be a wake-promoting neuropeptide with unknown mechanism, and a mutation in its receptor (NPSR1) causes the short sleep duration trait in humans. We investigated the role of different NPS+ nuclei in sleep/wake regulation. Loss-of-function and chemogenetic studies revealed that NPS+ neurons in the parabrachial nucleus (PB) are wake-promoting, whereas peri-locus coeruleus (peri-LC) NPS+ neurons are not important for sleep/wake modulation. Further, we found that a NPS+ nucleus in the central gray of the pons (CGPn) strongly promotes sleep. Fiber photometry recordings showed that NPS+ neurons are wake-active in the CGPn and wake/REM-sleep active in the PB and peri-LC. Blocking NPS-NPSR1 signaling or knockdown of Nps supported the function of the NPS-NPSR1 pathway in sleep/wake regulation. Together, these results reveal that NPS and NPS+ neurons play dichotomous roles in sleep/wake regulation at both the molecular and circuit levels.
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Affiliation(s)
- Lijuan Xing
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
| | - Xianlin Zou
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
| | - Chen Yin
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
| | - John M. Webb
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
| | - Guangsen Shi
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan528400, China
| | - Louis J. Ptáček
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94143
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA94143
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA94143
| | - Ying-Hui Fu
- Department of Neurology, University of California San Francisco, San Francisco, CA94143
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94143
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA94143
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA94143
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5
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Yang Z, Zhang Z, Li J, Chen W, Liu C. CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system. Brief Bioinform 2024; 25:bbae066. [PMID: 38426328 PMCID: PMC10905519 DOI: 10.1093/bib/bbae066] [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: 11/30/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
CRISPR/Cas9 is a promising RNA-guided genome editing technology, which consists of a Cas9 nuclease and a single-guide RNA (sgRNA). So far, a number of sgRNA prediction softwares have been developed. However, they were usually designed for protein-coding genes without considering that long non-coding RNA (lncRNA) genes may have different characteristics. In this study, we first evaluated the performances of a series of known sgRNA-designing tools in the context of both coding and non-coding datasets. Meanwhile, we analyzed the underpinnings of their varied performances on the sgRNA's specificity for lncRNA including nucleic acid sequence, genome location and editing mechanism preference. Furthermore, we introduce a support vector machine-based machine learning algorithm named CRISPRlnc, which aims to model both CRISPR knock-out (CRISPRko) and CRISPR inhibition (CRISPRi) mechanisms to predict the on-target activity of targets. CRISPRlnc combined the paired-sgRNA design and off-target analysis to achieve one-stop design of CRISPR/Cas9 sgRNAs for non-coding genes. Performance comparison on multiple datasets showed that CRISPRlnc was far superior to existing methods for both CRISPRko and CRISPRi mechanisms during the lncRNA-specific sgRNA design. To maximize the availability of CRISPRlnc, we developed a web server (http://predict.crisprlnc.cc) and made it available for download on GitHub.
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Affiliation(s)
- Zitian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zexin Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Chen
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, School of Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
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6
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Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [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: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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7
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Takahashi-Kanemitsu A, Lu M, Knight CT, Yamamoto T, Hayashi T, Mii Y, Ooki T, Kikuchi I, Kikuchi A, Barker N, Susaki EA, Taira M, Hatakeyama M. The Helicobacter pylori CagA oncoprotein disrupts Wnt/PCP signaling and promotes hyperproliferation of pyloric gland base cells. Sci Signal 2023; 16:eabp9020. [PMID: 37463245 DOI: 10.1126/scisignal.abp9020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/24/2023] [Indexed: 07/20/2023]
Abstract
Helicobacter pylori strains that deliver the oncoprotein CagA into gastric epithelial cells are the major etiologic agents of upper gastric diseases including gastric cancer. CagA promotes gastric carcinogenesis through interactions with multiple host proteins. Here, we show that CagA also disrupts Wnt-dependent planar cell polarity (Wnt/PCP), which orients cells within the plane of an epithelium and coordinates collective cell behaviors such as convergent extension to enable epithelial elongation during development. Ectopic expression of CagA in Xenopus laevis embryos impaired gastrulation, neural tube formation, and axis elongation, processes driven by convergent extension movements that depend on the Wnt/PCP pathway. Mice specifically expressing CagA in the stomach epithelium had longer pyloric glands and mislocalization of the tetraspanin proteins VANGL1 and VANGL2 (VANGL1/2), which are critical components of Wnt/PCP signaling. The increased pyloric gland length was due to hyperproliferation of cells at the gland base, where Lgr5+ stem and progenitor cells reside, and was associated with fewer differentiated enteroendocrine cells. In cultured human gastric epithelial cells, the N terminus of CagA interacted with the C-terminal cytoplasmic tails of VANGL1/2, which impaired Wnt/PCP signaling by inducing the mislocalization of VANGL1/2 from the plasma membrane to the cytoplasm. Thus, CagA may contribute to the development of gastric cancer by subverting a Wnt/PCP-dependent mechanism that restrains pyloric gland stem cell proliferation and promotes enteroendocrine differentiation.
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Affiliation(s)
- Atsushi Takahashi-Kanemitsu
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Mengxue Lu
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Christopher Takaya Knight
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Yamamoto
- Department of Biological Sciences, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Takuya Ooki
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Ippei Kikuchi
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka 565-0871, Japan
| | - Nick Barker
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Division of Epithelial Stem Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa 924-1192, Japan
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Masanori Hatakeyama
- Department of Microbiology, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory of Microbial Carcinogenesis, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Shinagawa-ku, Tokyo 141-0021, Japan
- Research Center of Microbial Carcinogenesis, Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido 060-0815, Japan
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8
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Tinoco A, Mitchison-Field L, Bradford J, Renicke C, Perrin D, Bay L, Pringle J, Cleves P. Role of the bicarbonate transporter SLC4γ in stony-coral skeleton formation and evolution. Proc Natl Acad Sci U S A 2023; 120:e2216144120. [PMID: 37276409 PMCID: PMC10268325 DOI: 10.1073/pnas.2216144120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023] Open
Abstract
Coral reefs are highly diverse ecosystems of immense ecological, economic, and aesthetic importance built on the calcium-carbonate-based skeletons of stony corals. The formation of these skeletons is threatened by increasing ocean temperatures and acidification, and a deeper understanding of the molecular mechanisms involved may assist efforts to mitigate the effects of such anthropogenic stressors. In this study, we focused on the role of the predicted bicarbonate transporter SLC4γ, which was suggested in previous studies to be a product of gene duplication and to have a role in coral-skeleton formation. Our comparative-genomics study using 30 coral species and 15 outgroups indicates that SLC4γ is present throughout the stony corals, but not in their non-skeleton-forming relatives, and apparently arose by gene duplication at the onset of stony-coral evolution. Our expression studies show that SLC4γ, but not the closely related and apparently ancestral SLC4β, is highly upregulated during coral development coincident with the onset of skeleton deposition. Moreover, we show that juvenile coral polyps carrying CRISPR/Cas9-induced mutations in SLC4γ are defective in skeleton formation, with the severity of the defect in individual animals correlated with their frequencies of SLC4γ mutations. Taken together, the results suggest that the evolution of the stony corals involved the neofunctionalization of the newly arisen SLC4γ for a unique role in the provision of concentrated bicarbonate for calcium-carbonate deposition. The results also demonstrate the feasibility of reverse-genetic studies of ecologically important traits in adult corals.
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Affiliation(s)
- Amanda I. Tinoco
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD21218
- Applied BioSciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lorna M. Y. Mitchison-Field
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD21218
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Jacob Bradford
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD4001, Australia
- School of Computer Science, Queensland University of Technology, Brisbane, QLD4001, Australia
| | - Christian Renicke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Dimitri Perrin
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD4001, Australia
- School of Computer Science, Queensland University of Technology, Brisbane, QLD4001, Australia
| | - Line K. Bay
- Australian Institute of Marine Science, Townsville, QLD4810, Australia
| | - John R. Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Phillip A. Cleves
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD21218
- Applied BioSciences, Macquarie University, Sydney, NSW2109, Australia
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
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9
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Dean B, Bakker G, Ueda HR, Tobin AB, Brown A, Kanaan RAA. A growing understanding of the role of muscarinic receptors in the molecular pathology and treatment of schizophrenia. Front Cell Neurosci 2023; 17:1124333. [PMID: 36909280 PMCID: PMC9992992 DOI: 10.3389/fncel.2023.1124333] [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: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Pre-clinical models, postmortem and neuroimaging studies all support a role for muscarinic receptors in the molecular pathology of schizophrenia. From these data it was proposed that activation of the muscarinic M1 and/or M4 receptor would reduce the severity of the symptoms of schizophrenia. This hypothesis is now supported by results from two clinical trials which indicate that activating central muscarinic M1 and M4 receptors can reduce the severity of positive, negative and cognitive symptoms of the disorder. This review will provide an update on a growing body of evidence that argues the muscarinic M1 and M4 receptors have critical roles in CNS functions that are dysregulated by the pathophysiology of schizophrenia. This realization has been made possible, in part, by the growing ability to visualize and quantify muscarinic M1 and M4 receptors in the human CNS using molecular neuroimaging. We will discuss how these advances have provided evidence to support the notion that there is a sub-group of patients within the syndrome of schizophrenia that have a unique molecular pathology driven by a marked loss of muscarinic M1 receptors. This review is timely, as drugs targeting muscarinic receptors approach clinical use for the treatment of schizophrenia and here we outline the background biology that supported development of such drugs to treat the disorder.
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Affiliation(s)
- Brian Dean
- Synaptic Biology and Cognition Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
| | | | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Andrew B Tobin
- Advanced Research Centre (ARC), School of Molecular Bioscience, University of Glasgow, Glasgow, United Kingdom
| | | | - Richard A A Kanaan
- Department of Psychiatry, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia
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10
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Koyanagi I, Tezuka T, Yu J, Srinivasan S, Naoi T, Yasugaki S, Nakai A, Taniguchi S, Hayashi Y, Nakano Y, Sakaguchi M. Fully automatic REM sleep stage-specific intervention systems using single EEG in mice. Neurosci Res 2023; 186:51-58. [PMID: 36206953 DOI: 10.1016/j.neures.2022.10.001] [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: 07/31/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Sleep stage-specific intervention is widely used to elucidate the functions of sleep and their underlying mechanisms. For this intervention, it is imperative to accurately classify rapid-eye-movement (REM) sleep. However, the proof of fully automatic real-time REM sleep classification in vivo has not been obtained in mice. Here, we report the in vivo implementation of a system that classifies sleep stages in real-time from a single-channel electroencephalogram (EEG). It enabled REM sleep-specific intervention with 90 % sensitivity and 86 % precision without prior configuration to each mouse. We further derived systems capable of classification with higher frequency sampling and time resolution. This attach-and-go sleep staging system provides a fully automatic accurate and scalable tool for investigating the functions of sleep.
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Affiliation(s)
- Iyo Koyanagi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Doctoral Program in Neuroscience, Degree Programs in Comprehensive Human Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Research Fellow of Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Taro Tezuka
- Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan.
| | - Jiahui Yu
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Doctoral Program in Neuroscience, Degree Programs in Comprehensive Human Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Sakthivel Srinivasan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Toshie Naoi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Shinnosuke Yasugaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Research Fellow of Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan; Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Ayaka Nakai
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Doctoral Program in Neuroscience, Degree Programs in Comprehensive Human Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Shimpei Taniguchi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan
| | - Yu Hayashi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yasushi Nakano
- Medical System Solutions II, KISSEI COMTEC CO., LTD, Matsumoto, Nagano 390-1293, Japan
| | - Masanori Sakaguchi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Doctoral Program in Neuroscience, Degree Programs in Comprehensive Human Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, 305-8575 Ibaraki, Japan; Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan.
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11
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Wang Y, Minami Y, Ode KL, Ueda HR. The role of calcium and CaMKII in sleep. Front Syst Neurosci 2022; 16:1059421. [PMID: 36618010 PMCID: PMC9815122 DOI: 10.3389/fnsys.2022.1059421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Sleep is an evolutionarily conserved phenotype shared by most of the animals on the planet. Prolonged wakefulness will result in increased sleep need or sleep pressure. However, its mechanisms remain elusive. Recent findings indicate that Ca2+ signaling, known to control diverse physiological functions, also regulates sleep. This review intends to summarize research advances in Ca2+ and Ca2+/calmodulin-dependent protein kinase II (CaMKII) in sleep regulation. Significant changes in sleep phenotype have been observed through calcium-related channels, receptors, and pumps. Mathematical modeling for neuronal firing patterns during NREM sleep suggests that these molecules compose a Ca2+-dependent hyperpolarization mechanism. The intracellular Ca2+ may then trigger sleep induction and maintenance through the activation of CaMKII, one of the sleep-promoting kinases. CaMKII and its multisite phosphorylation status may provide a link between transient calcium dynamics typically observed in neurons and sleep-wake dynamics observed on the long-time scale.
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Affiliation(s)
- Yuyang Wang
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koji L. Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Japan,*Correspondence: Hiroki R. Ueda,
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12
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Ozawa M, Taguchi J, Katsuma K, Ishikawa-Yamauchi Y, Kikuchi M, Sakamoto R, Yamada Y, Ikawa M. Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice. Sci Rep 2022; 12:21558. [PMID: 36513736 PMCID: PMC9748034 DOI: 10.1038/s41598-022-26107-z] [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: 03/18/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Gene targeting of embryonic stem (ES) cells followed by chimera production has been conventionally used for developing gene-manipulated mice. Although direct knock-in (KI) using murine zygote via CRISPR/Cas9-mediated genome editing has been reported, ES cell targeting still has merits, e.g., high throughput work can be performed in vitro. In this study, we first compared the KI efficiency of mouse ES cells with CRISPR/Cas9 expression vector and ribonucleoprotein (RNP), and confirmed that KI efficiency was significantly increased by using RNP. Using CRISPR/Cas9 RNP and circular plasmid with homologous arms as a targeting vector, knock-in within ES cell clones could be obtained efficiently without drug selection, thus potentially shortening the vector construction or cell culture period. Moreover, by incorporating a drug-resistant cassette into the targeting vectors, double DNA KI can be simultaneously achieved at high efficiency by a single electroporation. This technique will help to facilitate the production of genetically modified mouse models that are fundamental for exploring topics related to human and mammalian biology.
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Affiliation(s)
- Manabu Ozawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Jumpei Taguchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Kento Katsuma
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yu Ishikawa-Yamauchi
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Mio Kikuchi
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Reiko Sakamoto
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Yasuhiro Yamada
- grid.26999.3d0000 0001 2151 536XDivision of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Masahito Ikawa
- grid.26999.3d0000 0001 2151 536XLaboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan ,grid.136593.b0000 0004 0373 3971Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871 Japan
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13
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KOGASAKA Y, MURAKAMI S, YAMASHITA S, KIMURA D, FURUMOTO Y, IGUCHI K, SENDAI Y. Generation of germ cell-deficient pigs by NANOS3 knockout. J Reprod Dev 2022; 68:361-368. [PMID: 36273893 PMCID: PMC9792658 DOI: 10.1262/jrd.2022-028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
NANOS3 is an evolutionarily conserved gene expressed in primordial germ cells that is important for germ cell development. Germ cell deletion by NANOS3 knockout has been reported in several mammalian species, but its function in pigs is unclear. In the present study, we investigated the germline effects of NANOS3 knockout in pigs using CRISPR/Cas9. Embryo transfer of CRISPR/Cas9-modified embryos produced ten offspring, of which one showed wild-type NANOS3 alleles, eight had two mutant NANOS3 alleles, and the other exhibited mosaicism (four mutant alleles). Histological analysis revealed no germ cells in the testes or ovaries of any of the nine mutant pigs. These results demonstrated that NANOS3 is crucial for porcine germ cell production.
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Affiliation(s)
- Yuhei KOGASAKA
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Sho MURAKAMI
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Shiro YAMASHITA
- Quality Control Research Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Daisuke KIMURA
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Yoshinori FURUMOTO
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Kana IGUCHI
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
| | - Yutaka SENDAI
- Biological Sciences Section, Central Research Institute for Feed and Livestock, Zen-noh, Ibaraki 300-4204, Japan
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14
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A signalling pathway for transcriptional regulation of sleep amount in mice. Nature 2022; 612:519-527. [PMID: 36477534 DOI: 10.1038/s41586-022-05510-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
In mice and humans, sleep quantity is governed by genetic factors and exhibits age-dependent variation1-3. However, the core molecular pathways and effector mechanisms that regulate sleep duration in mammals remain unclear. Here, we characterize a major signalling pathway for the transcriptional regulation of sleep in mice using adeno-associated virus-mediated somatic genetics analysis4. Chimeric knockout of LKB1 kinase-an activator of AMPK-related protein kinase SIK35-7-in adult mouse brain markedly reduces the amount and delta power-a measure of sleep depth-of non-rapid eye movement sleep (NREMS). Downstream of the LKB1-SIK3 pathway, gain or loss-of-function of the histone deacetylases HDAC4 and HDAC5 in adult brain neurons causes bidirectional changes of NREMS amount and delta power. Moreover, phosphorylation of HDAC4 and HDAC5 is associated with increased sleep need, and HDAC4 specifically regulates NREMS amount in posterior hypothalamus. Genetic and transcriptomic studies reveal that HDAC4 cooperates with CREB in both transcriptional and sleep regulation. These findings introduce the concept of signalling pathways targeting transcription modulators to regulate daily sleep amount and demonstrate the power of somatic genetics in mouse sleep research.
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15
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Tone D, Ode KL, Zhang Q, Fujishima H, Yamada RG, Nagashima Y, Matsumoto K, Wen Z, Yoshida SY, Mitani TT, Arisato Y, Ohno RI, Ukai-Tadenuma M, Yoshida Garçon J, Kaneko M, Shi S, Ukai H, Miyamichi K, Okada T, Sumiyama K, Kiyonari H, Ueda HR. Distinct phosphorylation states of mammalian CaMKIIβ control the induction and maintenance of sleep. PLoS Biol 2022; 20:e3001813. [PMID: 36194579 PMCID: PMC9531794 DOI: 10.1371/journal.pbio.3001813] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
The reduced sleep duration previously observed in Camk2b knockout mice revealed a role for Ca2+/calmodulin-dependent protein kinase II (CaMKII)β as a sleep-promoting kinase. However, the underlying mechanism by which CaMKIIβ supports sleep regulation is largely unknown. Here, we demonstrate that activation or inhibition of CaMKIIβ can increase or decrease sleep duration in mice by almost 2-fold, supporting the role of CaMKIIβ as a core sleep regulator in mammals. Importantly, we show that this sleep regulation depends on the kinase activity of CaMKIIβ. A CaMKIIβ mutant mimicking the constitutive-active (auto)phosphorylation state promotes the transition from awake state to sleep state, while mutants mimicking subsequent multisite (auto)phosphorylation states suppress the transition from sleep state to awake state. These results suggest that the phosphorylation states of CaMKIIβ differently control sleep induction and maintenance processes, leading us to propose a "phosphorylation hypothesis of sleep" for the molecular control of sleep in mammals.
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Affiliation(s)
- Daisuke Tone
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Koji L. Ode
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Qianhui Zhang
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Yoshiki Nagashima
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Thermo Fisher Scientific K.K., Yokohama, Kanagawa, Japan
| | - Katsuhiko Matsumoto
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Zhiqing Wen
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shota Y. Yoshida
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Graduate school of Medicine, Osaka University, Suita, Osaka, Japan
| | - Tomoki T. Mitani
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Graduate school of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuki Arisato
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Rei-ichiro Ohno
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Maki Ukai-Tadenuma
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Junko Yoshida Garçon
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Kazunari Miyamichi
- Laboratory for Comparative Connections, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Takashi Okada
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, the University of Tokyo, Minato-city, Tokyo, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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16
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Liu Q. New advances in molecular and neural mechanisms of sleep regulation. BRAIN SCIENCE ADVANCES 2022. [DOI: 10.26599/bsa.2022.9050018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Qinghua Liu
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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17
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Abstract
Genetics is one of the various approaches adopted to understand and control mammalian sleep. Reverse genetics, which is usually applied to analyze sleep in gene-deficient mice, has been the mainstream field of genetic studies on sleep for the past three decades and has revealed that various molecules, including orexin, are involved in sleep regulation. Recently, forward genetic studies in humans and mice have identified gene mutations responsible for heritable sleep abnormalities, such as SIK3, NALCN, DEC2, the neuropeptide S receptor, and β1 adrenergic receptor. Furthermore, the protein kinase A-SIK3 pathway was shown to represent the intracellular neural signaling for sleep need. Large-scale genome-wide analyses of human sleep have been conducted, and many gene loci associated with individual differences in sleep have been found. The development of genome-editing technology and gene transfer by an adeno-associated virus has updated and expanded the genetic studies on mammals. These efforts are expected to elucidate the mechanisms of sleep–wake regulation and develop new therapeutic interventions for sleep disorders.
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Affiliation(s)
- Hiromasa Funato
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Department of Anatomy, Faculty of Medicine, Toho University, Ota-ku, Tokyo 951-8585, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas 75390, Texas, USA
- Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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18
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Genome-wide CRISPR screen for HSV-1 host factors reveals PAPSS1 contributes to heparan sulfate synthesis. Commun Biol 2022; 5:694. [PMID: 35854076 PMCID: PMC9296583 DOI: 10.1038/s42003-022-03581-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/10/2022] [Indexed: 12/01/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a ubiquitous pathogen that causes various diseases in humans, ranging from common mucocutaneous lesions to severe life-threatening encephalitis. However, our understanding of the interaction between HSV-1 and human host factors remains incomplete. Here, to identify the host factors for HSV-1 infection, we performed a human genome-wide CRISPR screen using near-haploid HAP1 cells, in which gene knockout (KO) could be efficiently achieved. Along with several already known host factors, we identified 3′-phosphoadenosine 5′-phosphosulfate synthase 1 (PAPSS1) as a host factor for HSV-1 infection. The KO of PAPSS1 in HAP1 cells reduced heparan sulfate (HepS) expression, consequently diminishing the binding of HSV-1 and several other HepS-dependent viruses (such as HSV-2, hepatitis B virus, and a human seasonal coronavirus). Hence, our findings provide further insights into the host factor requirements for HSV-1 infection and HepS biosynthesis. A genome-wide CRISPR screen for HSV-1 host factors using near-haploid HAP1 cells revealed PAPSS1 as an essential factor for heparan sulfate biosynthesis and HSV-1 infection, and identified several other host factors also involved in both processes.
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19
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Oginuma M, Nishida M, Ohmura-Adachi T, Abe K, Ogamino S, Mogi C, Matsui H, Ishitani T. Rapid reverse genetics systems for Nothobranchius furzeri, a suitable model organism to study vertebrate aging. Sci Rep 2022; 12:11628. [PMID: 35804091 PMCID: PMC9270483 DOI: 10.1038/s41598-022-15972-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
The African turquoise killifish Nothobranchius furzeri (N. furzeri) is a useful model organism for studying aging, age-related diseases, and embryonic diapause. CRISPR/Cas9-mediated gene knockout and Tol2 transposon-mediated transgenesis in N. furzeri have been reported previously. However, these methods take time to generate knockout and transgenic fish. In addition, knock-in technology that inserts large DNA fragments as fluorescent reporter constructs into the target gene in N. furzeri has not yet been established. Here, we show that triple-target CRISPR-mediated single gene disruption efficiently produces whole-body biallelic knockout and enables the examination of gene function in the F0 generation. In addition, we developed a method for creating the knock-in reporter N. furzeri without crossing by optimizing the CRISPR/Cas9 system. These methods drastically reduce the duration of experiments, and we think that these advances will accelerate aging and developmental studies using N. furzeri.
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Affiliation(s)
- Masayuki Oginuma
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Moana Nishida
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tomomi Ohmura-Adachi
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kota Abe
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shohei Ogamino
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.,Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Chihiro Mogi
- Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan. .,Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
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20
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Bradford J, Chappell T, Perrin D. Rapid Whole-Genome Identification of High Quality CRISPR Guide RNAs with the Crackling Method. CRISPR J 2022; 5:410-421. [PMID: 35686976 DOI: 10.1089/crispr.2021.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The design of CRISPR-Cas9 guide RNAs is not trivial and is a computationally demanding task. Design tools need to identify target sequences that will maximize the likelihood of obtaining the desired cut, while minimizing off-target risk. There is a need for a tool that can meet both objectives while remaining practical to use on large genomes. In this study, we present Crackling, a new method that is more suitable for meeting these objectives. We test its performance on 12 genomes and on data from validation studies. Crackling maximizes guide efficiency by combining multiple scoring approaches. On experimental data, the guides it selects are better than those selected by others. It also incorporates Inverted Signature Slice Lists (ISSL) for faster off-target scoring. ISSL provides a gain of an order of magnitude in speed compared with other popular tools, such as Cas-OFFinder, Crisflash, and FlashFry, while preserving the same level of accuracy. Overall, this makes Crackling a faster and better method to design guide RNAs at scale. Crackling is available at https://github.com/bmds-lab/Crackling under the Berkeley Software Distribution (BSD) 3-Clause license.
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Affiliation(s)
- Jacob Bradford
- School of Computer Science, Queensland University of Technology, Brisbane, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Timothy Chappell
- School of Computer Science, Queensland University of Technology, Brisbane, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, Brisbane, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, Queensland, Australia
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21
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The 103,200-arm acceleration dataset in the UK Biobank revealed a landscape of human sleep phenotypes. Proc Natl Acad Sci U S A 2022; 119:e2116729119. [PMID: 35302893 PMCID: PMC8944865 DOI: 10.1073/pnas.2116729119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceHuman sleep phenotypes are diversified by genetic and environmental factors, and a quantitative classification of sleep phenotypes would lead to the advancement of biomedical mechanisms underlying human sleep diversity. To achieve that, a pipeline of data analysis, including a state-of-the-art sleep/wake classification algorithm, the uniform manifold approximation and projection (UMAP) dimension reduction method, and the density-based spatial clustering of applications with noise (DBSCAN) clustering method, was applied to the 100,000-arm acceleration dataset. This revealed 16 clusters, including seven different insomnia-like phenotypes. This kind of quantitative pipeline of sleep analysis is expected to promote data-based diagnosis of sleep disorders and psychiatric disorders that tend to be complicated by sleep disorders.
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22
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Tsume-Kajioka M, Kimura-Yoshida C, Mochida K, Ueda Y, Matsuo I. BET proteins are essential for the specification and maintenance of the epiblast lineage in mouse preimplantation embryos. BMC Biol 2022; 20:64. [PMID: 35264162 PMCID: PMC8905768 DOI: 10.1186/s12915-022-01251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background During mammalian preimplantation development, as the fertilized egg develops and differentiates, three cell lineages become specified: trophectoderm (TE), epiblast, and primitive endoderm (PrE). Through two steps of cell fate decisions, 16-cell blastomeres develop into TE and an inner cell mass (ICM), and thereafter, the latter differentiates into pluripotent epiblast and PrE. Although bromodomain and extra-terminal domain (BET) proteins, such as BRD4, are necessary for the transcriptional activation of genes involved in the maintenance of mouse embryonic stem cells by occupying their enhancers, their roles in the development of mouse preimplantation are unknown. Results To evaluate the effect of BET protein deficiency on cell lineage formation, we cultured preimplantation embryos in the presence of JQ1, which blocks the binding of BET bromodomains to acetylated-histones. We found BET inhibition blocked the transcriptional activation of genes, such as Nanog, Otx2, and Sox2, important for the formation of the epiblast lineage in blastocysts. Expression studies with lineage-specific markers in morulae and blastocysts revealed BET proteins were essential for the specification and maintenance of the epiblast lineage but were dispensable for the formation of primarily extraembryonic TE and PrE lineages. Additional Ingenuity Pathway Analysis and expression studies with a transcriptionally active form of signal transducer and activator of the transcription 3 (STAT3) suggested BET-dependent activation was partly associated with the STAT3-dependent pathway to maintain the epiblast lineage. To identify BET proteins involved in the formation of the epiblast lineage, we analyzed mutant embryos deficient in Brd4, Brd2, and double mutants. Abolishment of NANOG-positive epiblast cells was only evident in Brd4/Brd2 double-deficient morulae. Thus, the phenotype of JQ1-treated embryos is reproduced not by a Brd4- or Brd2-single deficiency, but only Brd4/Brd2-double deficiency, demonstrating the redundant roles of BRD2 and BRD4 in the specification of the epiblast lineage. Conclusions BET proteins are essential to the specification and maintenance of the epiblast lineage by activating lineage-specific core transcription factors during mouse preimplantation development. Among BET proteins, BRD4 plays a central role and BRD2 a complementary role in the specification and maintenance of epiblast lineages. Additionally, BET-dependent maintenance of the epiblast lineage may be partly associated with the STAT3-dependent pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01251-0.
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Affiliation(s)
- Mami Tsume-Kajioka
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Chiharu Kimura-Yoshida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Kyoko Mochida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Yoko Ueda
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Isao Matsuo
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan. .,Department of Pediatric and Neonatal-Perinatal Research, Osaka Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
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23
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Minami Y, Yuan Y, Ueda HR. High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics. J Biol Rhythms 2022; 37:135-151. [PMID: 35137623 DOI: 10.1177/07487304221075002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Animal models are essential tools for modern scientists to conduct biological experiments and investigate their hypotheses in vivo. However, for the past decade, raising the throughput of such animal experiments has been a great challenge. Conventionally, in vivo high-throughput assay was achieved through large-scale mutagen-driven forward genetic screening, which took years to find causal genes. In contrast, reverse genetics accelerated the causal gene identification process, but its throughput was also limited by 2 barriers, that is, the genome modification step and the time-consuming crossing step. Defined as genetics without crossing, next-generation genetics is able to produce gene-modified animals that can be analyzed at the founder generation (F0). This method is or can be accomplished through recent technological advances in gene editing and virus-based efficient gene modifications. Notably, next-generation genetics has accelerated the process of cross-species studies, and it will be a useful technique during animal experiments as it can provide genetic perturbation at an individual level without crossing. In this review, we begin by introducing the history of animal-based high-throughput analysis, with a specific focus on chronobiology. We then describe ways that gene modification efficiency during animal experiments was enhanced and why crossing remained a barrier to reaching higher efficiency. Moreover, we mention the Triple CRISPR as a critical technique for achieving next-generation genetics. Finally, we discuss the potential applications and limitations of next-generation mammalian genetics.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
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24
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Fuselier KTB, Salbaum JM, Kappen C. Broad spectrum of CRISPR-induced edits in an embryonic lethal gene. Sci Rep 2021; 11:23732. [PMID: 34887431 PMCID: PMC8660864 DOI: 10.1038/s41598-021-02627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
Mendelian genetics poses practical limitations on the number of mutant genes that can be investigated simultaneously for their roles in embryonic development in the mouse. While CRISPR-based gene editing of multiple genes at once offers an attractive alternative strategy, subsequent breeding or establishment of permanent mouse lines will rapidly segregate the different mutant loci again. Direct phenotypic analysis of genomic edits in an embryonic lethal gene in F0 generation mice, or F0 mouse embryos, circumvents the need for breeding or establishment of mutant mouse lines. In the course of genotyping a large cohort of F0 CRISPants, where the embryonic lethal gene T/brachyury was targeted, we noted the presence of multiple CRISPR-induced modifications in individual embryos. Using long-read single-molecule Nanopore sequencing, we identified a wide variety of deletions, ranging up to 3 kb, that would not have been detected or scored as wildtype with commonly used genotyping methods that rely on subcloning and short-read or Sanger sequencing. Long-read sequencing results were crucial for accurate genotype-phenotype correlation in our F0 CRISPants. We thus demonstrate feasibility of screening manipulated F0 embryos for mid-gestation phenotypic consequences of CRISPR-induced mutations without requiring derivation of permanent mouse lines.
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Affiliation(s)
- Kayla T B Fuselier
- Department of Developmental Biology, Pennington Biomedical Research Center/Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA, 70808, USA
| | - J Michael Salbaum
- Department of Regulation of Gene Expression, Pennington Biomedical Research Center/Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA, 70808, USA
| | - Claudia Kappen
- Department of Developmental Biology, Pennington Biomedical Research Center/Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA, 70808, USA.
- Peggy M. Pennington Cole Chair in Developmental Biology, Pennington Biomedical Research Center/Louisiana State University System, 6400 Perkins Road, Baton Rouge, LA, 70808, USA.
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25
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Minami Y, Yuan Y, Ueda HR. Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling. Biophys Rev 2021; 13:1113-1126. [PMID: 35059031 PMCID: PMC8724464 DOI: 10.1007/s12551-021-00859-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
The system-level identification and analysis of molecular and cellular networks in mammals can be accelerated by "next-generation" genetics, which is defined as genetics that can achieve desired genetic makeup in a single generation without any animal crossing. We recently established a highly efficient procedure for producing knock-out (KO) mice using the "Triple-CRISPR" method, which targets a single gene by triple gRNAs in the CRISPR/Cas9 system. This procedure achieved an almost perfect KO efficiency (96-100%). We also established a highly efficient procedure, the "ES-mouse" method, for producing knock-in (KI) mice within a single generation. In this method, ES cells were treated with three inhibitors to keep their potency and then injected into 8-cell-stage embryos. These procedures dramatically shortened the time required to produce KO or KI mice from years down to about 3 months. The produced KO and KI mice can also be systematically profiled at a single-cell resolution by the "whole-organ cell profiling," which was realized by tissue-clearing methods, such as CUBIC, and an advanced light-sheet microscopy. The review describes the establishment and application of these technologies above in analyzing the three states (NREM sleep, REM sleep, and awake) of mammalian brains. It also discusses the role of calcium and muscarinic receptors in these states as well as the current challenges and future opportunities in the next-generation mammalian genetics and whole-organ cell profiling for organism-level systems biology.
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Affiliation(s)
- Yoichi Minami
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yufei Yuan
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Hiroki R. Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871 Japan
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26
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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27
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Webb JM, Fu YH. Recent advances in sleep genetics. Curr Opin Neurobiol 2021; 69:19-24. [PMID: 33360546 PMCID: PMC8217384 DOI: 10.1016/j.conb.2020.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/27/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022]
Abstract
Sleep regulation has a strong genetic component. In this review, we highlight the recent advances in sleep genetics from knockout, point mutation, and GWAS studies. We overview specific genetic effects on REM versus NREM sleep as well as how the implicated genes fall in broad functional categories. Furthermore, we elucidate how genes affect different aspects of sleep including sleep duration, sleep consolidation, recovery sleep, and the circadian timing of sleep, demonstrating that genetic studies can be powerful in understanding how the body regulates sleep.
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Affiliation(s)
- John M Webb
- Department of Neurology, Weill Institute for Neurosciences, Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ying-Hui Fu
- Department of Neurology, Weill Institute for Neurosciences, Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA 94143, USA.
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28
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Kiyonari H, Kaneko M, Abe T, Shiraishi A, Yoshimi R, Inoue KI, Furuta Y. Targeted gene disruption in a marsupial, Monodelphis domestica, by CRISPR/Cas9 genome editing. Curr Biol 2021; 31:3956-3963.e4. [PMID: 34293331 DOI: 10.1016/j.cub.2021.06.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/17/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022]
Abstract
Marsupials represent one of three extant mammalian subclasses with very unique characteristics not shared by other mammals. Most notably, much of the development of neonates immaturely born after a relatively short gestation takes place in the external environment. Among marsupials, the gray short-tailed opossum (Monodelphis domestica; hereafter "the opossum") is one of very few established laboratory models. Due to many biologically unique characteristics and experimentally advantageous features, the opossum is used as a prototype species for basic research on marsupial biology.1,2 However, in vivo studies of gene function in the opossum, and thus marsupials in general, lag far behind those of eutherian mammals due to the lack of reliable means to manipulate their genomes. In this study, we describe the successful generation of genome edited opossums by a combination of refined methodologies in reproductive biology and embryo manipulation. We took advantage of the opossum's resemblance to popular rodent models, such as the mouse and rat, in body size and breeding characteristics. First, we established a tractable pipeline of reproductive technologies, from induction of ovulation, timed copulation, and zygote collection to embryo transfer to pseudopregnant females, that warrant an essential platform to manipulate opossum zygotes. Further, we successfully demonstrated the generation of gene knockout opossums at the Tyr locus by microinjection of pronuclear stage zygotes using CRISPR/Cas9 genome editing, along with germline transmission of the edited alleles to the F1 generation. This study provides a critical foundation for venues to expand mammalian reverse genetics into the metatherian subclass.
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Affiliation(s)
- Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan.
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Aki Shiraishi
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Riko Yoshimi
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Ken-Ichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe 650-0047, Japan; Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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29
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Aihara S, Fujimoto S, Sakaguchi R, Imai T. BMPR-2 gates activity-dependent stabilization of primary dendrites during mitral cell remodeling. Cell Rep 2021; 35:109276. [PMID: 34161760 DOI: 10.1016/j.celrep.2021.109276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/28/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
Developing neurons initially form excessive neurites and then remodel them based on molecular cues and neuronal activity. Developing mitral cells in the olfactory bulb initially extend multiple primary dendrites. They then stabilize single primary dendrites while eliminating others. However, the mechanisms underlying selective dendrite remodeling remain elusive. Using CRISPR-Cas9-based knockout screening combined with in utero electroporation, we identify BMPR-2 as a key regulator for selective dendrite stabilization. Bmpr2 knockout and its rescue experiments show that BMPR-2 inhibits LIMK without ligands and thereby permits dendrite destabilization. In contrast, the overexpression of antagonists and agonists indicates that ligand-bound BMPR-2 stabilizes dendrites, most likely by releasing LIMK. Using genetic and FRET imaging experiments, we demonstrate that free LIMK is activated by NMDARs via Rac1, facilitating dendrite stabilization through F-actin formation. Thus, the selective stabilization of primary dendrites is ensured by concomitant inputs of BMP ligands and neuronal activity.
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Affiliation(s)
- Shuhei Aihara
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Satoshi Fujimoto
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Richi Sakaguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Takeshi Imai
- Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
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30
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Mano T, Murata K, Kon K, Shimizu C, Ono H, Shi S, Yamada RG, Miyamichi K, Susaki EA, Touhara K, Ueda HR. CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping. CELL REPORTS METHODS 2021; 1:100038. [PMID: 35475238 PMCID: PMC9017177 DOI: 10.1016/j.crmeth.2021.100038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 05/20/2021] [Indexed: 01/18/2023]
Abstract
Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.
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Affiliation(s)
- Tomoyuki Mano
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Ken Murata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazuhiro Kon
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Hiroaki Ono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
| | - Kazunari Miyamichi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Etsuo A. Susaki
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki R. Ueda
- Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-5241, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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31
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Miura K, Ogura A, Kobatake K, Honda H, Kaminuma O. Progress of genome editing technology and developmental biology useful for radiation research. JOURNAL OF RADIATION RESEARCH 2021; 62:i53-i63. [PMID: 33978171 PMCID: PMC8114227 DOI: 10.1093/jrr/rraa127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/26/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Following the development of genome editing technology, it has become more feasible to create genetically modified animals such as knockout (KO), knock-in, and point-mutated animals. The genome-edited animals are useful to investigate the roles of various functional genes in many fields of biological science including radiation research. Nevertheless, some researchers may experience difficulty in generating genome-edited animals, probably due to the requirement for equipment and techniques for embryo manipulation and handling. Furthermore, after obtaining F0 generation, genome-edited animals generally need to be expanded and maintained for analyzing the target gene function. To investigate genes essential for normal birth and growth, the generation of conditional KO (cKO) animals in which a tissue- or stage-specific gene mutation can be introduced is often required. Here, we describe the basic principle and application of genome editing technology including zinc-finger nuclease, transcription-activator-like effector nuclease, and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated protein (Cas) systems. Recently advanced developmental biology methods have enabled application of the technology, especially CRISPR/Cas, to zygotes, leading to the prompt production of genome-edited animals. For pre-implantation embryos, genome editing via oviductal nucleic acid delivery has been developed as an embryo manipulation- or handling-free method. Examining the gene function at F0 generation is becoming possible by employing triple-target CRISPR technology. This technology, in combination with a blastocyst complementation method enables investigation of even birth- and growth-responsible genes without establishing cKO strains. We hope that this review is helpful for understanding and expanding genome editing-related technology and for progressing radiation research.
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Affiliation(s)
- Kento Miura
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsuo Ogura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kohei Kobatake
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- Department of Urology, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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32
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Crawley O, Conde-Dusman MJ, Pérez-Otaño I. GluN3A NMDA receptor subunits: more enigmatic than ever? J Physiol 2021; 600:261-276. [PMID: 33942912 DOI: 10.1113/jp280879] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022] Open
Abstract
Non-conventional N-methyl-d-aspartate receptors (NMDARs) containing GluN3A subunits have unique biophysical, signalling and localization properties within the NMDAR family, and are typically thought to counterbalance functions of classical NMDARs made up of GluN1/2 subunits. Beyond their recognized roles in synapse refinement during postnatal development, recent evidence is building a wider perspective for GluN3A functions. Here we draw particular attention to the latest developments for this multifaceted and unusual subunit: from finely timed expression patterns that correlate with plasticity windows in developing brains or functional hierarchies in the mature brain to new insight onto presynaptic GluN3A-NMDARs, excitatory glycine receptors and behavioural impacts, alongside further connections to a range of brain disorders.
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Affiliation(s)
- Oliver Crawley
- Unidad de Neurobiología Celular y de Sistemas, Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante, 03550, Spain
| | - María J Conde-Dusman
- Unidad de Neurobiología Celular y de Sistemas, Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante, 03550, Spain
| | - Isabel Pérez-Otaño
- Unidad de Neurobiología Celular y de Sistemas, Instituto de Neurociencias (CSIC-UMH), San Juan de Alicante, 03550, Spain
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33
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Umemura K, Ohtsuki S, Nagaoka M, Kusamori K, Inoue T, Takahashi Y, Takakura Y, Nishikawa M. Critical contribution of macrophage scavenger receptor 1 to the uptake of nanostructured DNA by immune cells. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 34:102386. [PMID: 33774131 DOI: 10.1016/j.nano.2021.102386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 11/28/2022]
Abstract
Despite the efficient uptake of polypod-like nanostructured DNA, or polypodna, by macrophage-like RAW264.7 and other immune cells, the detailed mechanism has not been fully elucidated. Our previous study using HEK-Blue hTLR9 cells showed that transfection of macrophage scavenger receptor 1 (MSR1) increased the uptake of tetrapod-like structured DNA. Here, we investigated the involvement of MSR1 in the structure-dependent uptake of polypodna. Transfection of MSR1 to HEK-Blue hTLR9 cells pod number-dependently increased the uptake of polypodna, and its knockout in RAW264.7 cells reduced the uptake and subsequent cytokine release. To examine the binding of DNA with MSR1, biotinylated DNA added to RAW264.7 cells was cross-linked with cell surface proteins. Then, MSR1 cross-linked with polypodna, but not with single-stranded DNA. Similar results were obtained with murine primary immune cells. Taken together, MSR1 discriminates between simple and nanostructured DNAs and plays a dominant role in the efficient uptake of polypodna by immune cells.
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Affiliation(s)
- Keisuke Umemura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shozo Ohtsuki
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Makoto Nagaoka
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Kosuke Kusamori
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Takao Inoue
- Division of Cellular and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Makiya Nishikawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, Japan.
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34
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Lahtinen A, Häkkinen A, Puttonen S, Vanttola P, Viitasalo K, Porkka-Heiskanen T, Härmä M, Paunio T. Differential DNA methylation in recovery from shift work disorder. Sci Rep 2021; 11:2895. [PMID: 33536559 PMCID: PMC7858604 DOI: 10.1038/s41598-021-82627-0] [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: 10/07/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
The human DNA methylome is responsive to our environment, but its dynamics remain underexplored. We investigated the temporal changes to DNA methylation (DNAme) in relation to recovery from a shift work disorder (SWD) by performing a paired epigenome-wide analysis in an occupational cohort of 32 shift workers (25 men, age = 43.8 ± 8.8 years, 21 SWD cases). We found that the effect of vacation on DNAme was more prominent in the SWD-group as compared to controls, with respect to the amount of significantly differentially methylated positions (DMPs; Punadj < 0.05) 6.5 vs 3.7%, respectively. The vast majority (78%) of these DMPs were hypomethylated in SWD but not in controls (27%) during the work period. The Gene Ontology Cellular component "NMDA glutamate receptor" (PFDR < 0.05) was identified in a pathway analysis of the top 30 genes in SWD. In-depth pathway analyses revealed that the Reactome pathway "CREB phosphorylation through the activation of CaMKII" might underlie the recovery. Furthermore, three DMPs from this pathway, corresponding to GRIN2C, CREB1, and CAMK2B, correlated with the degree of recovery (Punadj < 0.05). Our findings provide evidence for the dynamic nature of DNAme in relation to the recovery process from a circadian disorder, with biological relevance of the emerging pathways.
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Affiliation(s)
- Alexandra Lahtinen
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland. .,Genomics and Biobank UnitDepartment of Public Health Solutions, Finnish Institute for Health and Welfare (THL), PO Box 30, 00271, Helsinki, Finland.
| | - Antti Häkkinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Puttonen
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | - Päivi Vanttola
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | | | - Tarja Porkka-Heiskanen
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Mikko Härmä
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | - Tiina Paunio
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland. .,Genomics and Biobank UnitDepartment of Public Health Solutions, Finnish Institute for Health and Welfare (THL), PO Box 30, 00271, Helsinki, Finland.
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35
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Kroll F, Powell GT, Ghosh M, Gestri G, Antinucci P, Hearn TJ, Tunbak H, Lim S, Dennis HW, Fernandez JM, Whitmore D, Dreosti E, Wilson SW, Hoffman EJ, Rihel J. A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes. eLife 2021; 10:e59683. [PMID: 33416493 PMCID: PMC7793621 DOI: 10.7554/elife.59683] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
Hundreds of human genes are associated with neurological diseases, but translation into tractable biological mechanisms is lagging. Larval zebrafish are an attractive model to investigate genetic contributions to neurological diseases. However, current CRISPR-Cas9 methods are difficult to apply to large genetic screens studying behavioural phenotypes. To facilitate rapid genetic screening, we developed a simple sequencing-free tool to validate gRNAs and a highly effective CRISPR-Cas9 method capable of converting >90% of injected embryos directly into F0 biallelic knockouts. We demonstrate that F0 knockouts reliably recapitulate complex mutant phenotypes, such as altered molecular rhythms of the circadian clock, escape responses to irritants, and multi-parameter day-night locomotor behaviours. The technique is sufficiently robust to knockout multiple genes in the same animal, for example to create the transparent triple knockout crystal fish for imaging. Our F0 knockout method cuts the experimental time from gene to behavioural phenotype in zebrafish from months to one week.
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Affiliation(s)
- François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gareth T Powell
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Marcus Ghosh
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Paride Antinucci
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Timothy J Hearn
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Hande Tunbak
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Sumi Lim
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Harvey W Dennis
- School of Biological Sciences, Faculty of Science, University of BristolBristolUnited Kingdom
| | | | - David Whitmore
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
- Department of Molecular and Cell Biology, James Cook UniversityTownsvilleAustralia
| | - Elena Dreosti
- Wolfson Institute for Biomedical Research, University College LondonLondonUnited Kingdom
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Ellen J Hoffman
- Child Study Center, Yale School of MedicineNew HavenUnited States
- Department of Neuroscience, Yale School of MedicineNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
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36
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Murillo A, Navarro AI, Puelles E, Zhang Y, Petros TJ, Pérez-Otaño I. Temporal Dynamics and Neuronal Specificity of Grin3a Expression in the Mouse Forebrain. Cereb Cortex 2020; 31:1914-1926. [PMID: 33290502 PMCID: PMC7945027 DOI: 10.1093/cercor/bhaa330] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
GluN3A subunits endow N-Methyl-D-Aspartate receptors (NMDARs) with unique biophysical, trafficking, and signaling properties. GluN3A-NMDARs are typically expressed during postnatal development, when they are thought to gate the refinement of neural circuits by inhibiting synapse maturation, and stabilization. Recent work suggests that GluN3A also operates in adult brains to control a variety of behaviors, yet a full spatiotemporal characterization of GluN3A expression is lacking. Here, we conducted a systematic analysis of Grin3a (gene encoding mouse GluN3A) mRNA expression in the mouse brain by combining high-sensitivity colorimetric and fluorescence in situ hybridization with labeling for neuronal subtypes. We find that, while Grin3a mRNA expression peaks postnatally, significant levels are retained into adulthood in specific brain regions such as the amygdala, medial habenula, association cortices, and high-order thalamic nuclei. The time-course of emergence and down-regulation of Grin3a expression varies across brain region, cortical layer of residence, and sensory modality, in a pattern that correlates with previously reported hierarchical gradients of brain maturation and functional specialization. Grin3a is expressed in both excitatory and inhibitory neurons, with strong mRNA levels being a distinguishing feature of somatostatin interneurons. Our study provides a comprehensive map of Grin3a distribution across the murine lifespan and paves the way for dissecting the diverse functions of GluN3A in health and disease.
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Affiliation(s)
- Alvaro Murillo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas - Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain.,UK Dementia Research Institute at Cardiff University, CF24 4HQ Cardiff, UK
| | - Ana I Navarro
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas - Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
| | - Eduardo Puelles
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas - Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
| | - Yajun Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Timothy J Petros
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Isabel Pérez-Otaño
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas - Universidad Miguel Hernández, 03550 Sant Joan d'Alacant, Spain
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37
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Nishizono H, Yasuda R, Laviv T. Methodologies and Challenges for CRISPR/Cas9 Mediated Genome Editing of the Mammalian Brain. Front Genome Ed 2020; 2:602970. [PMID: 34713226 PMCID: PMC8525404 DOI: 10.3389/fgeed.2020.602970] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
Neurons and glia are highly polarized cells with extensive subcellular structures extending over large distances from their cell bodies. Previous research has revealed elaborate protein signaling complexes localized within intracellular compartments. Thus, exploring the function and the localization of endogenous proteins is vital to understanding the precise molecular mechanisms underlying the synapse, cellular, and circuit function. Recent advances in CRISPR/Cas9-based genome editing techniques have allowed researchers to rapidly develop transgenic animal models and perform single-cell level genome editing in the mammalian brain. Here, we introduce and comprehensively review the latest techniques for genome-editing in whole animals using fertilized eggs and methods for gene editing in specific neuronal populations in the adult or developing mammalian brain. Finally, we describe the advantages and disadvantages of each technique, as well as the challenges that lie ahead to advance the generation of methodologies for genome editing in the brain using the current CRISPR/Cas9 system.
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Affiliation(s)
- Hirofumi Nishizono
- Department of Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, FL, United States
| | - Ryohei Yasuda
- Department of Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, FL, United States
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38
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Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proc Natl Acad Sci U S A 2020; 117:28899-28905. [PMID: 33168726 DOI: 10.1073/pnas.1920779117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reef-building corals are keystone species that are threatened by anthropogenic stresses including climate change. To investigate corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating many hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals or closely related cnidarians. CRISPR technology seems likely to alleviate this problem. Indeed, we show here that microinjection of single-guide RNA/Cas9 ribonucleoprotein complexes into fertilized eggs of the coral Acropora millepora can produce a sufficiently high frequency of mutations to detect a clear phenotype in the injected generation. Based in part on experiments in a sea-anemone model system, we targeted the gene encoding Heat Shock Transcription Factor 1 (HSF1) and obtained larvae in which >90% of the gene copies were mutant. The mutant larvae survived well at 27 °C but died rapidly at 34 °C, a temperature that did not produce detectable mortality over the duration of the experiment in wild-type (WT) larvae or larvae injected with Cas9 alone. We conclude that HSF1 function (presumably its induction of genes in response to heat stress) plays an important protective role in corals. More broadly, we conclude that CRISPR mutagenesis in corals should allow wide-ranging and rigorous tests of gene function in both larval and adult corals.
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39
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Funano SI, Tone D, Ukai H, Ueda HR, Tanaka Y. Rapid and easy-to-use ES cell manipulation device with a small groove near culturing wells. BMC Res Notes 2020; 13:453. [PMID: 33012292 PMCID: PMC7534166 DOI: 10.1186/s13104-020-05294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/15/2020] [Indexed: 11/11/2022] Open
Abstract
Objective Production of genetically modified mice including Knock-out (KO) or Knock-in (KI) mice is necessary for organism-level phenotype analysis. Embryonic stem cell (ESC)-based technologies can produce many genetically modified mice with less time without crossing. However, a complicated manual operation is required to increase the number of ESC colonies. Here, the objective of this study was to design and demonstrate a new device to easily find colonies and carry them to microwells. Results We developed a polydimethylsiloxane-based device for easy manipulation and isolation of ESC colonies. By introducing ESC colonies into the groove placed near culturing microwells, users can easily find, pick up and carry ESC colonies to microwells. By hydrophilic treatment using bovine serum albumin, 2-μL droplets including colonies reached the microwell bottom. Operation time using this device was shortened for both beginners (2.3-fold) and experts (1.5-fold) compared to the conventional colony picking operation. Isolated ESC colonies were confirmed to have maintained pluripotency. This device is expected to promote research by shortening the isolation procedure for ESC colonies or other large cells (e.g. eggs or embryos) and shortening training time for beginners as a simple sorter.
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Affiliation(s)
- Shun-Ichi Funano
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Tone
- Laboratory for Synthetic Biology, Center for Biosystems Dynamics Research, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hideki Ukai
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, Center for Biosystems Dynamics Research, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research, RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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40
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Abstract
Sleep is a fundamental property conserved across species. The homeostatic induction of sleep indicates the presence of a mechanism that is progressively activated by the awake state and that induces sleep. Several lines of evidence support that such function, namely, sleep need, lies in the neuronal assemblies rather than specific brain regions and circuits. However, the molecular mechanism underlying the dynamics of sleep need is still unclear. This review aims to summarize recent studies mainly in rodents indicating that protein phosphorylation, especially at the synapses, could be the molecular entity associated with sleep need. Genetic studies in rodents have identified a set of kinases that promote sleep. The activity of sleep-promoting kinases appears to be elevated during the awake phase and in sleep deprivation. Furthermore, the proteomic analysis demonstrated that the phosphorylation status of synaptic protein is controlled by the sleep-wake cycle. Therefore, a plausible scenario may be that the awake-dependent activation of kinases modifies the phosphorylation status of synaptic proteins to promote sleep. We also discuss the possible importance of multisite phosphorylation on macromolecular protein complexes to achieve the slow dynamics and physiological functions of sleep in mammals.
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Affiliation(s)
- Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics, Osaka, Japan
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41
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Miura K, Matoba S, Hirose M, Ogura A. Generation of chimeric mice with spermatozoa fully derived from embryonic stem cells using a triple-target CRISPR method for Nanos3†. Biol Reprod 2020; 104:223-233. [PMID: 32965494 PMCID: PMC7786261 DOI: 10.1093/biolre/ioaa176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/02/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Conditional knockout (cKO) mice have contributed greatly to understanding the tissue- or stage-specific functions of genes in vivo. However, the current cKO method requires considerable time and effort because of the need to generate two gene-modified mouse strains (Cre transgenic and loxP knockin) for crossing. Here, we examined whether we could analyze the germ cell-related functions of embryonic lethal genes in F0 chimeric mice by restricting the origin of germ cells to mutant embryonic stem cells (ESCs). We confirmed that the full ESC origin of spermatozoa in fertile chimeric mice was achieved by the CRISPR/Cas9 system using three guide RNAs targeting Nanos3, which induced germ cell depletion in the host blastocyst-derived tissues. Among these fertile chimeric mice, those from male ESCs with a Dnmt3b mutation, which normally causes embryo death, also produced F1 mice derived exclusively from the mutant ESCs. Thus, our new chimeric strategy readily revealed that Dnmt3b is dispensable for male germ cell development, in agreement with a previous cKO study. Our new approach enables us to analyze the germ cell functions of embryonic lethal genes in the F0 generation without using the current cKO method.
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Affiliation(s)
- Kento Miura
- RIKEN BioResource Research Center, Ibaraki, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shogo Matoba
- RIKEN BioResource Research Center, Ibaraki, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Atsuo Ogura
- RIKEN BioResource Research Center, Ibaraki, Japan.,RIKEN Cluster for Pioneering Research, Saitama, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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42
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Takahashi TM, Sunagawa GA, Soya S, Abe M, Sakurai K, Ishikawa K, Yanagisawa M, Hama H, Hasegawa E, Miyawaki A, Sakimura K, Takahashi M, Sakurai T. A discrete neuronal circuit induces a hibernation-like state in rodents. Nature 2020; 583:109-114. [PMID: 32528181 DOI: 10.1038/s41586-020-2163-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/04/2020] [Indexed: 02/07/2023]
Abstract
Hibernating mammals actively lower their body temperature to reduce energy expenditure when facing food scarcity1. This ability to induce a hypometabolic state has evoked great interest owing to its potential medical benefits2,3. Here we show that a hypothalamic neuronal circuit in rodents induces a long-lasting hypothermic and hypometabolic state similar to hibernation. In this state, although body temperature and levels of oxygen consumption are kept very low, the ability to regulate metabolism still remains functional, as in hibernation4. There was no obvious damage to tissues and organs or abnormalities in behaviour after recovery from this state. Our findings could enable the development of a method to induce a hibernation-like state, which would have potential applications in non-hibernating mammalian species including humans.
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Affiliation(s)
- Tohru M Takahashi
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Genshiro A Sunagawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Shingo Soya
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Katsuyasu Sakurai
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Kiyomi Ishikawa
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Hama
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Japan
| | - Emi Hasegawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masayo Takahashi
- Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Takeshi Sakurai
- Faculty of Medicine, University of Tsukuba, Tsukuba, Japan. .,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan. .,Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan.
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43
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Batra T, Malik I, Prabhat A, Bhardwaj SK, Kumar V. Sleep in unnatural times: illuminated night negatively affects sleep and associated hypothalamic gene expressions in diurnal zebra finches. Proc Biol Sci 2020; 287:20192952. [PMID: 32517617 DOI: 10.1098/rspb.2019.2952] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We investigated the effects of exposure at ecologically relevant levels of dim light at night (dLAN) on sleep and the 24 h hypothalamic expression pattern of genes involved in the circadian timing (per2, bmal1, reverb-β, cry1, ror-α, clock) and sleep regulatory pathways (cytokines: tlr4, tnf-α, il-1β, nos; Ca2+-dependent pathway: camk2, sik3, nr3a; cholinergic receptor, achm3) in diurnal female zebra finches. Birds were exposed to 12 h light (150 lux) coupled with 12 h of absolute darkness or of 5 lux dim light for three weeks. dLAN fragmented the nocturnal sleep in reduced bouts, and caused sleep loss as evidenced by reduced plasma oxalate levels. Under dLAN, the 24 h rhythm of per2, but not bmal1 or reverb-β, showed a reduced amplitude and altered peak expression time; however, clock, ror-α and cry1 expressions showed an abolition of the 24 h rhythm. Decreased tlr4, il-1β and nos, and the lack of diurnal difference in achm3 messenger RNA levels suggested an attenuated inhibition of the arousal system (hence, awake state promotion) under dLAN. Similarly, changes in camk2, sik3 and nr3a expressions suggested dLAN-effects on Ca2+-dependent sleep-inducing pathways. These results demonstrate dLAN-induced negative effects on sleep and associated hypothalamic molecular pathways, and provide insights into health risks of illuminated night exposures to diurnal animals.
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Affiliation(s)
- Twinkle Batra
- Department of Zoology, University of Delhi, Delhi 110 007, India
| | - Indu Malik
- Department of Zoology, University of Delhi, Delhi 110 007, India
| | - Abhilash Prabhat
- Department of Zoology, University of Delhi, Delhi 110 007, India
| | | | - Vinod Kumar
- Department of Zoology, University of Delhi, Delhi 110 007, India
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Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas. Nat Commun 2020; 11:2150. [PMID: 32358519 PMCID: PMC7195362 DOI: 10.1038/s41467-020-16044-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 04/07/2020] [Indexed: 01/31/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) in mammals is an inefficient process that is frequently associated with abnormal phenotypes, especially in placentas. Recent studies demonstrated that mouse SCNT placentas completely lack histone methylation (H3K27me3)-dependent imprinting, but how it affects placental development remains unclear. Here, we provide evidence that the loss of H3K27me3 imprinting is responsible for abnormal placental enlargement and low birth rates following SCNT, through upregulation of imprinted miRNAs. When we restore the normal paternal expression of H3K27me3-dependent imprinted genes (Sfmbt2, Gab1, and Slc38a4) in SCNT placentas by maternal knockout, the placentas remain enlarged. Intriguingly, correcting the expression of clustered miRNAs within the Sfmbt2 gene ameliorates the placental phenotype. Importantly, their target genes, which are confirmed to cause SCNT-like placental histology, recover their expression level. The birth rates increase about twofold. Thus, we identify loss of H3K27me3 imprinting as an epigenetic error that compromises embryo development following SCNT. Somatic cell nuclear transfer (SCNT) frequently results in abnormal placenta development in cloned mice. Here the authors show that loss of histone methylation (H3K27me3) imprinting in clustered Sfmbt2 miRNAs contributes to SCNT placenta defect.
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Abstract
Sleep is a ubiquitous and complex behavior in both its manifestation and regulation. Despite its essential role in maintaining optimal performance, health, and well-being, the genetic mechanisms underlying sleep remain poorly understood. Here, we review the forward genetic approaches undertaken in the last four years to elucidate the genes and gene pathways affecting sleep and its regulation. Despite an increasing number of studies and mining large databases, a coherent picture on “sleep” genes has yet to emerge. We highlight the results achieved by using unbiased genetic screens mainly in humans, mice, and fruit flies with an emphasis on normal sleep and make reference to lessons learned from the circadian field.
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Affiliation(s)
- Maxime Jan
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Bruce F O'Hara
- Department of Biology, University of Kentucky, Lexington, 40515, USA
| | - Paul Franken
- Centre for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
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Argentati C, Tortorella I, Bazzucchi M, Morena F, Martino S. Harnessing the Potential of Stem Cells for Disease Modeling: Progress and Promises. J Pers Med 2020; 10:E8. [PMID: 32041088 PMCID: PMC7151621 DOI: 10.3390/jpm10010008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/18/2020] [Accepted: 02/01/2020] [Indexed: 12/11/2022] Open
Abstract
Ex vivo cell/tissue-based models are an essential step in the workflow of pathophysiology studies, assay development, disease modeling, drug discovery, and development of personalized therapeutic strategies. For these purposes, both scientific and pharmaceutical research have adopted ex vivo stem cell models because of their better predictive power. As matter of a fact, the advancing in isolation and in vitro expansion protocols for culturing autologous human stem cells, and the standardization of methods for generating patient-derived induced pluripotent stem cells has made feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Furthermore, the potential of stem cells on generating more complex systems, such as scaffold-cell models, organoids, or organ-on-a-chip, allowed to overcome the limitations of the two-dimensional culture systems as well as to better mimic tissues structures and functions. Finally, the advent of genome-editing/gene therapy technologies had a great impact on the generation of more proficient stem cell-disease models and on establishing an effective therapeutic treatment. In this review, we discuss important breakthroughs of stem cell-based models highlighting current directions, advantages, and limitations and point out the need to combine experimental biology with computational tools able to describe complex biological systems and deliver results or predictions in the context of personalized medicine.
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Affiliation(s)
- Chiara Argentati
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Via del Giochetto, 06126 Perugia, Italy; (C.A.); (I.T.); (M.B.); (F.M.)
| | - Ilaria Tortorella
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Via del Giochetto, 06126 Perugia, Italy; (C.A.); (I.T.); (M.B.); (F.M.)
| | - Martina Bazzucchi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Via del Giochetto, 06126 Perugia, Italy; (C.A.); (I.T.); (M.B.); (F.M.)
| | - Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Via del Giochetto, 06126 Perugia, Italy; (C.A.); (I.T.); (M.B.); (F.M.)
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Via del Giochetto, 06126 Perugia, Italy; (C.A.); (I.T.); (M.B.); (F.M.)
- CEMIN, Center of Excellence on Nanostructured Innovative Materials, Via del Giochetto, 06126 Perugia, Italy
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Niwa Y, Kanda GN, Yamada RG, Shi S, Sunagawa GA, Ukai-Tadenuma M, Fujishima H, Matsumoto N, Masumoto KH, Nagano M, Kasukawa T, Galloway J, Perrin D, Shigeyoshi Y, Ukai H, Kiyonari H, Sumiyama K, Ueda HR. Muscarinic Acetylcholine Receptors Chrm1 and Chrm3 Are Essential for REM Sleep. Cell Rep 2020; 24:2231-2247.e7. [PMID: 30157420 DOI: 10.1016/j.celrep.2018.07.082] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/03/2018] [Accepted: 07/25/2018] [Indexed: 01/30/2023] Open
Abstract
Sleep regulation involves interdependent signaling among specialized neurons in distributed brain regions. Although acetylcholine promotes wakefulness and rapid eye movement (REM) sleep, it is unclear whether the cholinergic pathway is essential (i.e., absolutely required) for REM sleep because of redundancy from neural circuits to molecules. First, we demonstrate that synaptic inhibition of TrkA+ cholinergic neurons causes a severe short-sleep phenotype and that sleep reduction is mostly attributable to a shortened sleep duration in the dark phase. Subsequent comprehensive knockout of acetylcholine receptor genes by the triple-target CRISPR method reveals that a similar short-sleep phenotype appears in the knockout of two Gq-type acetylcholine receptors Chrm1 and Chrm3. Strikingly, Chrm1 and Chrm3 double knockout chronically diminishes REM sleep to an almost undetectable level. These results suggest that muscarinic acetylcholine receptors, Chrm1 and Chrm3, are essential for REM sleep.
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Affiliation(s)
- Yasutaka Niwa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Institute for Integrative Sleep Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Genki N Kanda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shoi Shi
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Genshiro A Sunagawa
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Maki Ukai-Tadenuma
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naomi Matsumoto
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Koh-Hei Masumoto
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan; Center for Medical Science, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan; Division of Neuroanatomy, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Mianmi-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
| | - Takeya Kasukawa
- Large Scale Data Managing Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - James Galloway
- School of Electrical Engineering and Computer Science, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Dimitri Perrin
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; School of Electrical Engineering and Computer Science, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
| | - Hideki Ukai
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Kiyonari
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Abstract
Rapid-eye movement (REM) sleep is a paradoxical sleep state characterized by brain activity similar to wakefulness, rapid-eye-movement, and lack of muscle tone. REM sleep is a fundamental brain function, evolutionary conserved across species, including human, mouse, bird, and even reptiles. The physiological importance of REM sleep is highlighted by severe sleep disorders incurred by a failure in REM sleep regulation. Despite the intense interest in the mechanism of REM sleep regulation, the molecular machinery is largely left to be investigated. In models of REM sleep regulation, acetylcholine has been a pivotal component. However, even newly emerged techniques such as pharmacogenetics and optogenetics have not fully clarified the function of acetylcholine either at the cellular level or neural-circuit level. Recently, we discovered that the Gq type muscarinic acetylcholine receptor genes, Chrm1 and Chrm3, are essential for REM sleep. In this review, we develop the perspective of current knowledge on REM sleep from a molecular viewpoint. This should be a starting point to clarify the molecular and cellular machinery underlying REM sleep regulation and will provide insights to explore physiological functions of REM sleep and its pathological roles in REM-sleep-related disorders such as depression, PTSD, and neurodegenerative diseases.
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Affiliation(s)
- Rikuhiro G Yamada
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan.,Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Bradford J, Perrin D. Improving CRISPR guide design with consensus approaches. BMC Genomics 2019; 20:931. [PMID: 31874627 PMCID: PMC6929336 DOI: 10.1186/s12864-019-6291-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022] Open
Abstract
Background CRISPR-based systems are playing an important role in modern genome engineering. A large number of computational methods have been developed to assist in the identification of suitable guides. However, there is only limited overlap between the guides that each tool identifies. This can motivate further development, but also raises the question of whether it is possible to combine existing tools to improve guide design. Results We considered nine leading guide design tools, and their output when tested using two sets of guides for which experimental validation data is available. We found that consensus approaches were able to outperform individual tools. The best performance (with a precision of up to 0.912) was obtained when combining four of the tools and accepting all guides selected by at least three of them. Conclusions These results can be used to improve CRISPR-based studies, but also to guide further tool development. However, they only provide a short-term solution as the time and computational resources required to run four tools may be impractical in certain applications.
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Affiliation(s)
- Jacob Bradford
- School of Electrical Engineering and Computer Science, Science and Engineering Faculty, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Dimitri Perrin
- School of Electrical Engineering and Computer Science, Science and Engineering Faculty, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia.
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50
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Fumoto K, Takigawa-Imamura H, Sumiyama K, Yoshimura SH, Maehara N, Kikuchi A. Mark1 regulates distal airspace expansion through type I pneumocyte flattening in lung development. J Cell Sci 2019; 132:jcs.235556. [PMID: 31719161 DOI: 10.1242/jcs.235556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
During the later stages of lung development, two types of pneumocytes, cuboidal type II (AECII) and flattened type I (AECI) alveolar epithelial cells, form distal lung saccules. Here, we highlight how fibroblasts expressing MAP-microtubule affinity regulating kinase 1 (Mark1) are required for the terminal stages of pulmonary development, called lung sacculation. In Mark1-knockout (KO) mice, distal sacculation and AECI flattening are significantly impaired. Fetal epithelial cells generate alveolar organoids and differentiate into pneumocytes when co-cultured with fibroblasts. However, the size of organoids decreased and AECI flattening was impaired in the presence of Mark1 KO fibroblasts. In Mark1 KO fibroblasts themselves, cilia formation and the Hedgehog pathway were suppressed, resulting in the loss of type I collagen expression. The addition of type I collagen restored AECI flattening in organoids co-cultured with Mark1 KO fibroblasts and rescued the decreased size of organoids. Mathematical modeling of distal lung sacculation supports the view that AECI flattening is necessary for the proper formation of saccule-like structures. These results suggest that Mark1-mediated fibroblast activation induces AECI flattening and thereby regulates distal lung sacculation.
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Affiliation(s)
- Katsumi Fumoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Hisako Takigawa-Imamura
- Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Natsumi Maehara
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
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