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Sato M, Fukuda K, Kadota M, Makino-Itou H, Tatsumi K, Yamauchi S, Kuraku S. Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. DNA Res 2024; 31:dsae004. [PMID: 38451834 DOI: 10.1093/dnares/dsae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asia. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to ~30-folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards 'telomere-to-telomere' sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions were predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.
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Affiliation(s)
- Mana Sato
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuya Fukuda
- Laboratory of Reproductive Physiology of Aquatic Organisms, School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hatsune Makino-Itou
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Shinya Yamauchi
- Fukushima Marine Science Museum (Aquamarine Fukushima), Iwaki, Fukushima, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
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Nakamura T, Yoshihara T, Tanegashima C, Kadota M, Kobayashi Y, Honda K, Ishiwata M, Ueda J, Hara T, Nakanishi M, Takumi T, Itohara S, Kuraku S, Asano M, Kasahara T, Nakajima K, Tsuboi T, Takata A, Kato T. Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor. Mol Psychiatry 2024:10.1038/s41380-024-02479-8. [PMID: 38528071 DOI: 10.1038/s41380-024-02479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways, KMT2C, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how KMT2C haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated. To address this, we developed and analyzed genetically engineered mice with a heterozygous frameshift mutation of Kmt2c (Kmt2c+/fs mice) as a disease model with high etiological validity. In a series of behavioral analyses, the mutant mice exhibit autistic-like behaviors such as impairments in sociality, flexibility, and working memory, demonstrating their face validity as an ASD model. To investigate the molecular basis of the observed abnormalities, we performed a transcriptomic analysis of their bulk adult brains and found that ASD risk genes were specifically enriched in the upregulated differentially expressed genes (DEGs), whereas KMT2C peaks detected by ChIP-seq were significantly co-localized with the downregulated genes, suggesting an important role of putative indirect effects of Kmt2c haploinsufficiency. We further performed single-cell RNA sequencing of newborn mouse brains to obtain cell type-resolved insights at an earlier stage. By integrating findings from ASD exome sequencing, genome-wide association, and postmortem brain studies to characterize DEGs in each cell cluster, we found strong ASD-associated transcriptomic changes in radial glia and immature neurons with no obvious bias toward upregulated or downregulated DEGs. On the other hand, there was no significant gross change in the cellular composition. Lastly, we explored potential therapeutic agents and demonstrate that vafidemstat, a lysine-specific histone demethylase 1 (LSD1) inhibitor that was effective in other models of neuropsychiatric/neurodevelopmental disorders, ameliorates impairments in sociality but not working memory in adult Kmt2c+/fs mice. Intriguingly, the administration of vafidemstat was shown to alter the vast majority of DEGs in the direction to normalize the transcriptomic abnormalities in the mutant mice (94.3 and 82.5% of the significant upregulated and downregulated DEGs, respectively, P < 2.2 × 10-16, binomial test), which could be the molecular mechanism underlying the behavioral rescuing. In summary, our study expands the repertoire of ASD models with high etiological and face validity, elucidates the cell-type resolved molecular alterations due to Kmt2c haploinsufficiency, and demonstrates the efficacy of an LSD1 inhibitor that might be generalizable to multiple categories of psychiatric disorders along with a better understanding of its presumed mechanisms of action.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Yuki Kobayashi
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Moe Nakanishi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Mechanism of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Hyogo, Japan
| | - Shigeyoshi Itohara
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kazuo Nakajima
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan.
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Bilgic M, Wu Q, Suetsugu T, Shitamukai A, Tsunekawa Y, Shimogori T, Kadota M, Nishimura O, Kuraku S, Kiyonari H, Matsuzaki F. Truncated radial glia as a common precursor in the late corticogenesis of gyrencephalic mammals. eLife 2023; 12:RP91406. [PMID: 37988289 PMCID: PMC10662950 DOI: 10.7554/elife.91406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
The diversity of neural stem cells is a hallmark of the cerebral cortex development in gyrencephalic mammals, such as Primates and Carnivora. Among them, ferrets are a good model for mechanistic studies. However, information on their neural progenitor cells (NPC), termed radial glia (RG), is limited. Here, we surveyed the temporal series of single-cell transcriptomes of progenitors regarding ferret corticogenesis and found a conserved diversity and temporal trajectory between human and ferret NPC, despite the large timescale difference. We found truncated RG (tRG) in ferret cortical development, a progenitor subtype previously described in humans. The combination of in silico and in vivo analyses identified that tRG differentiate into both ependymal and astrogenic cells. Via transcriptomic comparison, we predict that this is also the case in humans. Our findings suggest that tRG plays a role in the formation of adult ventricles, thereby providing the architectural bases for brain expansion.
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Affiliation(s)
- Merve Bilgic
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School for Biostudies, Kyoto UniversityKyotoJapan
| | - Quan Wu
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Taeko Suetsugu
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Atsunori Shitamukai
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Yuji Tsunekawa
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Tomomi Shimogori
- Molecular Mechanisms of Brain Development, RIKEN Center for Brain ScienceWakoJapan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Fumio Matsuzaki
- Laboratory for Cell Asymmetry, RIKEN Center for Biosystems Dynamics ResearchKobeJapan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School for Biostudies, Kyoto UniversityKyotoJapan
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4
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Yamaguchi K, Uno Y, Kadota M, Nishimura O, Nozu R, Murakumo K, Matsumoto R, Sato K, Kuraku S. Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization. Genome Res 2023; 33:1527-1540. [PMID: 37591668 PMCID: PMC10620051 DOI: 10.1101/gr.276840.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus Our analysis using a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes show a gradualism of chromosome length with remarkable length-dependent characteristics-shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in nonmammalian vertebrates. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced at high quality.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Yoshinobu Uno
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
| | | | | | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
- Okinawa Churaumi Aquarium, 905-0206, Okinawa, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan;
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, 411-8540, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), 411-8540, Mishima, Japan
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Enomoto Y, Katsura H, Fujimura T, Ogata A, Baba S, Yamaoka A, Kihara M, Abe T, Nishimura O, Kadota M, Hazama D, Tanaka Y, Maniwa Y, Nagano T, Morimoto M. Autocrine TGF-β-positive feedback in profibrotic AT2-lineage cells plays a crucial role in non-inflammatory lung fibrogenesis. Nat Commun 2023; 14:4956. [PMID: 37653024 PMCID: PMC10471635 DOI: 10.1038/s41467-023-40617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
The molecular etiology of idiopathic pulmonary fibrosis (IPF) has been extensively investigated to identify new therapeutic targets. Although anti-inflammatory treatments are not effective for patients with IPF, damaged alveolar epithelial cells play a critical role in lung fibrogenesis. Here, we establish an organoid-based lung fibrosis model using mouse and human lung tissues to assess the direct communication between damaged alveolar type II (AT2)-lineage cells and lung fibroblasts by excluding immune cells. Using this in vitro model and mouse genetics, we demonstrate that bleomycin causes DNA damage and activates p53 signaling in AT2-lineage cells, leading to AT2-to-AT1 transition-like state with a senescence-associated secretory phenotype (SASP). Among SASP-related factors, TGF-β plays an exclusive role in promoting lung fibroblast-to-myofibroblast differentiation. Moreover, the autocrine TGF-β-positive feedback loop in AT2-lineage cells is a critical cellular system in non-inflammatory lung fibrogenesis. These findings provide insights into the mechanism of IPF and potential therapeutic targets.
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Affiliation(s)
- Yasunori Enomoto
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Hiroaki Katsura
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takashi Fujimura
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Department of Drug Modality Development, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co., Ltd., 5-1-35 Saitoaokita, Minoh, 562-0029, Japan
| | - Akira Ogata
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Saori Baba
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Akira Yamaoka
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering (LARGE), RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering (LARGE), RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Daisuke Hazama
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yugo Tanaka
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yoshimasa Maniwa
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Tatsuya Nagano
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Mitsuru Morimoto
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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Sakaguchi S, Mizuno S, Okochi Y, Tanegashima C, Nishimura O, Uemura T, Kadota M, Naoki H, Kondo T. Single-cell transcriptome atlas of Drosophila gastrula 2.0. Cell Rep 2023:112707. [PMID: 37433294 DOI: 10.1016/j.celrep.2023.112707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023] Open
Abstract
During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing accurate spatial and lineage information are still lacking. Here, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. We find that the expression profiles of plasma-membrane-related genes, but not those of transcription-factor genes, represent each germ layer, supporting the nonequivalent contribution of each transcription-factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstruct the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.
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Affiliation(s)
- Shunta Sakaguchi
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sonoko Mizuno
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Okochi
- Laboratory of Theoretical Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tadashi Uemura
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Center for Living Systems Information Science, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Honda Naoki
- Laboratory of Theoretical Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Laboratory of Data-driven Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan; Theoretical Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Takefumi Kondo
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Sakyo-ku, Kyoto 606-8501, Japan.
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7
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Nishimura O, Rozewicki J, Yamaguchi K, Tatsumi K, Ohishi Y, Ohta T, Yagura M, Niwa T, Tanegashima C, Teramura A, Hirase S, Kawaguchi A, Tan M, D'Aniello S, Castro F, Machado A, Koyanagi M, Terakita A, Misawa R, Horie M, Kawasaki J, Asahida T, Yamaguchi A, Murakumo K, Matsumoto R, Irisarri I, Miyamoto N, Toyoda A, Tanaka S, Sakamoto T, Semba Y, Yamauchi S, Yamada K, Nishida K, Kiyatake I, Sato K, Hyodo S, Kadota M, Uno Y, Kuraku S. Squalomix: shark and ray genome analysis consortium and its data sharing platform. F1000Res 2022; 11:1077. [PMID: 36262334 PMCID: PMC9561540 DOI: 10.12688/f1000research.123591.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.
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Affiliation(s)
- Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - John Rozewicki
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Tazro Ohta
- Joint Support-Center for Data Science Research, Database Center for Life Science, Mishima, Shizuoka, 411-8540, Japan
| | - Masaru Yagura
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Taiki Niwa
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Akinori Teramura
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Akane Kawaguchi
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy
| | - Filipe Castro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal,Faculty of Sciences, University of Porto, Porto, Portugal
| | - André Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Ryo Misawa
- Japan Fisheries Research and Education Agency, Hachinohe, Aomori, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Junna Kawasaki
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Takashi Asahida
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuko Yamaguchi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Nagasaki, Japan
| | | | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature-Zoology, Hamburg, 20146, Germany
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Sho Tanaka
- School of Marine Science and Technology, Tokai University, Shizuoka, Shizuoka, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Graduate School of Natural Science and Technology, Okayama University, Setouchi, Japan., Okayama, Japan
| | - Yasuko Semba
- Highly Migratory Resources Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shizuoka, Shizuoka, Japan
| | | | - Kazuyuki Yamada
- Marine Science Museum, Tokai University, Shizuoka, Shizuoka, Japan
| | | | | | - Keiichi Sato
- Okinawa Churaumi Aquarium, Motobu, Okinawa, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo,, Kashiwa, Chiba, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan
| | - Yoshinobu Uno
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, 657-0024, Japan,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan,
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8
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Aburatani N, Takagi W, Wong MKS, Kuraku S, Tanegashima C, Kadota M, Saito K, Godo W, Sakamoto T, Hyodo S. Molecular and morphological investigations on the renal mechanisms enabling euryhalinity of red stingray Hemitrygon akajei. Front Physiol 2022; 13:953665. [PMID: 36017340 PMCID: PMC9396271 DOI: 10.3389/fphys.2022.953665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Most cartilaginous fishes live in seawater (SW), but a few exceptional elasmobranchs (sharks and rays) are euryhaline and can acclimate to freshwater (FW) environments. The plasma of elasmobranchs is high in NaCl and urea concentrations, which constrains osmotic water loss. However, these euryhaline elasmobranchs maintain high levels of plasma NaCl and urea even when acclimating to low salinity, resulting in a strong osmotic gradient from external environment to body fluid. The kidney consequently produces a large volume of dilute urine to cope with the water influx. In the present study, we investigated the molecular mechanisms of dilute urine production in the kidney of Japanese red stingray, Hemitrygon akajei, transferred from SW to low-salinity environments. We showed that red stingray maintained high plasma NaCl and urea levels by reabsorbing more osmolytes in the kidney when transferred to low salinity. RNA-seq and qPCR analyses were conducted to identify genes involved in NaCl and urea reabsorption under the low-salinity conditions, and the upregulated gene expressions of Na+-K+-Cl- cotransporter 2 (nkcc2) and Na+/K+-ATPase (nka) were found in the FW-acclimated individuals. These upregulations occurred in the early distal tubule (EDT) in the bundle zone of the kidney, which coils around the proximal and collecting tubules to form the highly convoluted structure of batoid nephron. Considering the previously proposed model for urea reabsorption, the upregulation of nkcc2 and nka not only causes the reabsorption of NaCl in the EDT, but potentially also supports enhanced urea reabsorption and eventually the production of dilute urine in FW-acclimated individuals. We propose advantageous characteristics of the batoid-type nephron that facilitate acclimation to a wide range of salinities, which might have allowed the batoids to expand their habitats.
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Affiliation(s)
- Naotaka Aburatani
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- *Correspondence: Naotaka Aburatani, ; Wataru Takagi,
| | - Wataru Takagi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- *Correspondence: Naotaka Aburatani, ; Wataru Takagi,
| | - Marty Kwok-Shing Wong
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Kazuhiro Saito
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Japan
| | - Waichiro Godo
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Faculty of Science, Okayama University, Setouchi, Japan
| | - Susumu Hyodo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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9
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Yamaguchi K, Wakatsuki T, Okushi Y, Suto K, Matsumoto K, Takahashi T, Kadota M, Kawabata Y, Matsuura T, Ise T, Kusunose K, Yagi S, Yamada H, Soeki T, Sata M. Early and chronic phased local coagulative responses following bioresorbable-polymer drug-eluting stent implantation. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Neointimal maturation after bioresorbable-polymer (BP) drug-eluting stent (DES) implantation will not be complete in the absorption phase of the polymer. We have previously reported local persistent hypercoagulation after sirolimus-eluting stent (SES) implantation by measuring local plasma prothrombin fragment 1+2 (F1+2) levels. The aim of this study is to examine time-dependent local coagulative response after BP-DES implantation.
Methods
Sixty-four patients who were treated about ten months earlier with coronary angioplasty, with no evidence of restenosis, were studied [durable-polymer (DP)-DES {SES; Cypher®: 26pts and everolimus-eluting stent (EES); Xience®: 16pts} and BP-DES (BP-EES; Synergy®: 10pts and BP-SES; Ultimaster®: 12pts)]. We measured plasma levels of F1+2 sampled in coronary sinus (CS) and sinus of Valsalva (V) at the early (2±1 months) and chronic (10±2 months) phases. The transcardiac gradient (Δ) was defined as CS level minus V level.
Results
No significant differences were observed in the percent diameter stenosis between the DP- and BP- DES groups (11.5±15.5 vs 14.1±11.9%). The ΔF1+2 was significantly lower in the BP-DES group than in the DP-DES group at the chronic phase (7.5±16.1 vs 16.4±17.1pmol/l, p<0.05). In the BP-DES group, the ΔF1+2 did not differ significantly between the early and chronic phases (7.0±14.1 vs 7.5±16.1pmol/l, NS).
Conclusion
Lower local coagulative response was observed at the chronic phase after BP-DES implantation compared to DP-DES implantation, and local hypercoagulation after BP-DES implantation was not observed at the early phase compared to the chronic phase. These findings might lead to the possibility of shorter dual antiplatelet therapy after BP-DES implantation.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- K Yamaguchi
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - T Wakatsuki
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - Y Okushi
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - K Suto
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - K Matsumoto
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - T Takahashi
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - M Kadota
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - Y Kawabata
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - T Matsuura
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - T Ise
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - K Kusunose
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - S Yagi
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - H Yamada
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - T Soeki
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
| | - M Sata
- Department of Cardiovascular Medicine, Tokushima University Hospital, Tokushima, Japan
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10
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Yamaguchi K, Kadota M, Nishimura O, Ohishi Y, Naito Y, Kuraku S. Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies. Mol Ecol 2021; 30:5923-5934. [PMID: 34432923 PMCID: PMC9292758 DOI: 10.1111/mec.16146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
The recent development of ecological studies has been fueled by the introduction of massive information based on chromosome‐scale genome sequences, even for species for which genetic linkage is not accessible. This was enabled mainly by the application of Hi‐C, a method for genome‐wide chromosome conformation capture that was originally developed for investigating the long‐range interaction of chromatins. Performing genomic scaffolding using Hi‐C data is highly resource‐demanding and employs elaborate laboratory steps for sample preparation. It starts with building a primary genome sequence assembly as an input, which is followed by computation for genome scaffolding using Hi‐C data, requiring careful validation. This article presents technical considerations for obtaining optimal Hi‐C scaffolding results and provides a test case of its application to a reptile species, the Madagascar ground gecko (Paroedura picta). Among the metrics that are frequently used for evaluating scaffolding results, we investigate the validity of the completeness assessment of chromosome‐scale genome assemblies using single‐copy reference orthologues.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuta Ohishi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yuki Naito
- Database Center for Life Science (DBCLS), Mishima, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
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11
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Jayakumar V, Nishimura O, Kadota M, Hirose N, Sano H, Murakawa Y, Yamamoto Y, Nakaya M, Tsukiyama T, Seita Y, Nakamura S, Kawai J, Sasaki E, Ema M, Kuraku S, Kawaji H, Sakakibara Y. Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset. Sci Data 2021; 8:159. [PMID: 34183680 PMCID: PMC8239027 DOI: 10.1038/s41597-021-00935-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/29/2021] [Indexed: 01/18/2023] Open
Abstract
Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.
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Affiliation(s)
- Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Naoki Hirose
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiromi Sano
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Center for Integrative Medical Sciences RIKEN-IFOM Joint Laboratory for Cancer Genomics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences RIKEN-IFOM Joint Laboratory for Cancer Genomics, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Yumiko Yamamoto
- RIKEN Center for Integrative Medical Sciences Laboratory for Comprehensive Genomic Analysis, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masataka Nakaya
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Tomoyuki Tsukiyama
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Yasunari Seita
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Shinichiro Nakamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Jun Kawai
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Erika Sasaki
- Central Institute for Experimental Animals, Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, 3-25-12, Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, 520-2192, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Science Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan.
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12
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Ohnishi T, Kiyama Y, Arima‐Yoshida F, Kadota M, Ichikawa T, Yamada K, Watanabe A, Ohba H, Tanaka K, Nakaya A, Horiuchi Y, Iwayama Y, Toyoshima M, Ogawa I, Shimamoto‐Mitsuyama C, Maekawa M, Balan S, Arai M, Miyashita M, Toriumi K, Nozaki Y, Kurokawa R, Suzuki K, Yoshikawa A, Toyota T, Hosoya T, Okuno H, Bito H, Itokawa M, Kuraku S, Manabe T, Yoshikawa T. Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia. EMBO Mol Med 2021; 13:e12574. [PMID: 33656268 PMCID: PMC8033514 DOI: 10.15252/emmm.202012574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/15/2023] Open
Abstract
Genomic defects with large effect size can help elucidate unknown pathologic architecture of mental disorders. We previously reported on a patient with schizophrenia and a balanced translocation between chromosomes 4 and 13 and found that the breakpoint within chromosome 4 is located near the LDB2 gene. We show here that Ldb2 knockout (KO) mice displayed multiple deficits relevant to mental disorders. In particular, Ldb2 KO mice exhibited deficits in the fear-conditioning paradigm. Analysis of the amygdala suggested that dysregulation of synaptic activities controlled by the immediate early gene Arc is involved in the phenotypes. We show that LDB2 forms protein complexes with known transcription factors. Consistently, ChIP-seq analyses indicated that LDB2 binds to > 10,000 genomic sites in human neurospheres. We found that many of those sites, including the promoter region of ARC, are occupied by EGR transcription factors. Our previous study showed an association of the EGR family genes with schizophrenia. Collectively, the findings suggest that dysregulation in the gene expression controlled by the LDB2-EGR axis underlies a pathogenesis of subset of mental disorders.
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13
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Onimaru K, Tatsumi K, Tanegashima C, Kadota M, Nishimura O, Kuraku S. Developmental hourglass and heterochronic shifts in fin and limb development. eLife 2021; 10:62865. [PMID: 33560225 PMCID: PMC7932699 DOI: 10.7554/elife.62865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here, we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open-chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls. Animals come in all shapes and sizes. This diversity arose through genetic mutations during evolution, but it is unclear exactly how these variations led to the formation of new shapes. There is increasing evidence to suggest that not all shapes are possible and that variability between animals is limited by a phenomenon known as “developmental constraint”. These limitations direct parts of the body towards a specific shape as they develop in the embryo. Therefore, understanding the mechanisms underlying these developmental constraints could help explain how different body shapes evolved. The limbs of humans and other mammals evolved from the fins of fish, and this transition is often used to study the role developmental constraints play in evolution. This is an ideal model as there is already a detailed fossil record mapping this evolutionary event, and data pinpointing some of the genes involved in the development of limbs and fins. But this data is incomplete, and a full comparison between the genes activated in the fin and the limb during embryonic development had not been achieved. This is because most fish used for research have undergone recent genetic changes, making it hard to spot which genetic differences are linked to the evolution of the limb. To overcome this barrier, Onimaru et al. compared genetic data from the developing limbs of mice to the developing fins of the brown-banded bamboo shark, which evolves much slower than other fish. This revealed that although many genes commonly played a role in the development of the fin and the limb in the embryo, the activity of these shared genes was not the same. For example, genes that switched on in the late stages of limb development, switched off in the late stages of fin development. But in the middle of development, those differences were relatively small and both species activated very similar sets of genes. Many of these genes were pleiotropic, which means they have important roles in other tissues and therefore mutate less often. This suggests that the mid-stage of limb development is under the strongest level of constraint. Darwin’s theory of natural selection explains that mutations drive evolution. But the theory cannot predict what kinds of new body shapes new mutations will produce. Understanding how the activity levels of different genes affect development could help to fill this knowledge gap. This has potential medical applications, for example, understanding why some genetic changes cause more serious problems than others. This work suggests that mutations in genes that are active during the mid-stage of limb development may have the most serious impact.
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Affiliation(s)
- Koh Onimaru
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,Laboratory for Bioinformatics Research, RIKEN BDR, Wako City, Japan.,Molecular Oncology Laboratory, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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14
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Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? Gigascience 2020; 9:5695848. [PMID: 31919520 PMCID: PMC6952475 DOI: 10.1093/gigascience/giz158] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/23/2019] [Accepted: 12/02/2019] [Indexed: 12/28/2022] Open
Abstract
Background Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. Results To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage. Conclusions This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Kaori Tanaka
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
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15
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Aburatani N, Takagi W, Wong MKS, Kadota M, Kuraku S, Tokunaga K, Kofuji K, Saito K, Godo W, Sakamoto T, Hyodo S. Facilitated NaCl Uptake in the Highly Developed Bundle of the Nephron in Japanese Red Stingray Hemitrygon akajei Revealed by Comparative Anatomy and Molecular Mapping. Zoolog Sci 2020; 37:458-466. [PMID: 32972087 DOI: 10.2108/zs200038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/08/2020] [Indexed: 11/17/2022]
Abstract
Batoidea (rays and skates) is a monophyletic subgroup of elasmobranchs that diverged from the common ancestor with Selachii (sharks) about 270 Mya. A larger number of batoids can adapt to low-salinity environments, in contrast to sharks, which are mostly stenohaline marine species. Among osmoregulatory organs of elasmobranchs, the kidney is known to be dedicated to urea retention in ureosmotic cartilaginous fishes. However, we know little regarding urea reabsorbing mechanisms in the kidney of batoids. Here, we performed physiological and histological investigations on the nephrons in the red stingray (Hemitrygon akajei) and two shark species. We found that the urine/plasma ratios of salt and urea concentrations in the stingray are significantly lower than those in cloudy catshark (Scyliorhinus torazame) under natural seawater, indicating that the kidney of stingray more strongly reabsorbs these osmolytes. By comparing the three-dimensional images of nephrons between stingray and banded houndshark (Triakis scyllium), we showed that the tubular bundle of stingray has a more compact configuration. In the compact tubular bundle of stingray kidney, the distal diluting tubule was highly developed and frequently coiled around the proximal and collecting tubules. Furthermore, co-expression of NKAα1 (Na+/K +-ATPase) and NKCC2 (Na+- K+-2Cl- cotransporter 2) mRNAs was prominent in the coiled diluting segment. These findings imply that NaCl reabsorption is greatly facilitated in the stingray kidney, resulting in a higher reabsorption rate of urea. Lowering the loss of osmolytes in the glomerular filtrate is likely favorable to the adaptability of batoids to a wide range of environmental salinity.
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Affiliation(s)
- Naotaka Aburatani
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan,
| | - Wataru Takagi
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan,
| | - Marty Kwok-Sing Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics, Kobe 650-0047, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics, Kobe 650-0047, Japan
| | | | - Kazuya Kofuji
- Ibaraki Prefectural Oarai Aquarium, Oarai 311-1301, Japan
| | - Kazuhiro Saito
- Ushimado Marine Institute, Faculty of Science,Okayama University, Ushimado 701-4303, Japan
| | - Waichiro Godo
- Ushimado Marine Institute, Faculty of Science,Okayama University, Ushimado 701-4303, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Faculty of Science,Okayama University, Ushimado 701-4303, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
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16
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Kusakabe R, Higuchi S, Tanaka M, Kadota M, Nishimura O, Kuratani S. Novel developmental bases for the evolution of hypobranchial muscles in vertebrates. BMC Biol 2020; 18:120. [PMID: 32907560 PMCID: PMC7488077 DOI: 10.1186/s12915-020-00851-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Vertebrates are characterized by possession of hypobranchial muscles (HBMs). Cyclostomes, or modern jawless vertebrates, possess a rudimentary and superficial HBM lateral to the pharynx, whereas the HBM in jawed vertebrates is internalized and anteroposteriorly specified. Precursor cells of the HBM, marked by expression of Lbx1, originate from somites and undergo extensive migration before becoming innervated by the hypoglossal nerve. How the complex form of HBM arose in evolution is relevant to the establishment of the vertebrate body plan, but despite having long been assumed to be similar to that of limb muscles, modification of developmental mechanisms of HBM remains enigmatic. RESULTS Here we characterize the expression of Lbx genes in lamprey and hagfish (cyclostomes) and catshark (gnathostome; jawed vertebrates). We show that the expression patterns of the single cyclostome Lbx homologue, Lbx-A, do not resemble the somitic expression of mammalian Lbx1. Disruption of Lbx-A revealed that LjLbx-A is required for the formation of both HBM and body wall muscles, likely due to the insufficient extension of precursor cells rather than to hindered muscle differentiation. Both homologues of Lbx in the catshark were expressed in the somitic muscle primordia, unlike in amniotes. During catshark embryogenesis, Lbx2 is expressed in the caudal HBM as well as in the abdominal rectus muscle, similar to lamprey Lbx-A, whereas Lbx1 marks the rostral HBM and pectoral fin muscle. CONCLUSIONS We conclude that the vertebrate HBM primarily emerged as a specialized somatic muscle to cover the pharynx, and the anterior internalized HBM of the gnathostomes is likely a novelty added rostral to the cyclostome-like HBM, for which duplication and functionalization of Lbx genes would have been a prerequisite.
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Affiliation(s)
- Rie Kusakabe
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Shinnosuke Higuchi
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Masako Tanaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, 650-0047, Japan
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Abstract
Epigenetic regulation plays central roles in gene expression. Since histone modification was discovered in the 1960s, its physiological and pathological functions have been extensively studied. Indeed, the advent of next-generation deep sequencing and chromatin immunoprecipitation (ChIP) via specific histone modification antibodies has revolutionized our view of epigenetic regulation across the genome. Conversely, tissues typically consist of diverse cell types, and their complex mixture poses analytic challenges to investigating the epigenome in a particular cell type. To address the cell type-specific chromatin state in a genome-wide manner, we recently developed tandem chromatin immunoprecipitation sequencing (tChIP-Seq), which is based on the selective purification of chromatin by tagged core histone proteins from cell types of interest, followed by ChIP-Seq. The goal of this protocol is the introduction of best practices of tChIP-Seq. This technique provides a versatile tool for tissue-specific epigenome investigation in diverse histone modifications and model organisms.
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Affiliation(s)
- Mari Mito
- RNA Biology Laboratory, RIKEN; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN; RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University;
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo;
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18
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Tanegashima C, Nishimura O, Motone F, Tatsumi K, Kadota M, Kuraku S. Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. Sci Data 2018; 5:180200. [PMID: 30295675 PMCID: PMC6174922 DOI: 10.1038/sdata.2018.200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/31/2018] [Indexed: 11/09/2022] Open
Abstract
Chondrichthyans (cartilaginous fishes) exhibit highly variable reproductive styles, categorized as viviparity and oviparity. Among these, species with oviparity provide an enormous potential of molecular experimentation with stable sample supply which does not demand the sacrifices of live mothers. Cartilaginous fishes are divided into two subclasses, chimaeras (Holocephali) and elasmobranchs (Elasmobranchii), and the latter consists of two monophyletic groups, Batoidea (rays, skates and torpedoes) and Selachimorpha (sharks). Here we report transcriptome assemblies of the ocellate spot skate Okamejei kenojei, produced by strand-specific RNA-seq of its embryonic tissues. We obtained a total of 325 million illumina short reads from libraries prepared using four different tissue domains and assembled them all together. Our assembly result confirmed the species authenticity and high continuity of contig sequences. Also, assessment of its coverage of pre-selected one-to-one orthologs supported high diversity of transcripts in the assemblies. Our products are expected to provide a basis of comparative molecular studies encompassing other chondrichthyan species with emerging genomic and transcriptomic sequence information.
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Affiliation(s)
- Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Fumio Motone
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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19
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Nabeshima R, Nishimura O, Maeda T, Shimizu N, Ide T, Yashiro K, Sakai Y, Meno C, Kadota M, Shiratori H, Kuraku S, Hamada H. Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters. eLife 2018; 7:36435. [PMID: 30070635 PMCID: PMC6072441 DOI: 10.7554/elife.36435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/10/2018] [Indexed: 01/28/2023] Open
Abstract
We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a-/- embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a-/- embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at E9.5 in Fam60a-/- embryos, suggesting that DNA demethylation is enhanced in the mutant. Examination of genome-wide DNA methylation identified several differentially methylated regions, which were preferentially hypomethylated, in Fam60a-/- embryos. Our data suggest that Fam60a is required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation at specific gene promoters.
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Affiliation(s)
- Ryo Nabeshima
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Osamu Nishimura
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Takako Maeda
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Natsumi Shimizu
- Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Takahiro Ide
- Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Kenta Yashiro
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasuo Sakai
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Chikara Meno
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Mitsutaka Kadota
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Hidetaka Shiratori
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Hiroshi Hamada
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory for Organismal Patterning, RIKEN Center for Developmental Biology, Kobe, Japan
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20
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Mito M, Kadota M, Tanaka K, Furuta Y, Abe K, Iwasaki S, Nakagawa S. Cell Type-Specific Survey of Epigenetic Modifications by Tandem Chromatin Immunoprecipitation Sequencing. Sci Rep 2018; 8:1143. [PMID: 29348483 PMCID: PMC5773701 DOI: 10.1038/s41598-018-19494-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022] Open
Abstract
The nervous system of higher eukaryotes is composed of numerous types of neurons and glia that together orchestrate complex neuronal responses. However, this complex pool of cells typically poses analytical challenges in investigating gene expression profiles and their epigenetic basis for specific cell types. Here, we developed a novel method that enables cell type-specific analyses of epigenetic modifications using tandem chromatin immunoprecipitation sequencing (tChIP-Seq). FLAG-tagged histone H2B, a constitutive chromatin component, was first expressed in Camk2a-positive pyramidal cortical neurons and used to purify chromatin in a cell type-specific manner. Subsequent chromatin immunoprecipitation using antibodies against H3K4me3-a chromatin modification mainly associated with active promoters-allowed us to survey the histone modifications in Camk2a-positive neurons. Indeed, tChIP-Seq identified hundreds of H3K4me3 modifications in promoter regions located upstream of genes associated with neuronal functions and genes with unknown functions in cortical neurons. tChIP-Seq provides a versatile approach to investigating the epigenetic modifications of particular cell types in vivo.
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Affiliation(s)
- Mari Mito
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.,RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Mitsutaka Kadota
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kaori Tanaka
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-Minamimachi, Chuou-ku, Kobe, 650-0047, Japan
| | - Yasuhide Furuta
- Animal Resource Development Unit and RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, 650-0047, Japan
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 2-1 Hirosawa, Wako, 351-0198, Japan.
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan. .,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
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21
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Hu N, Kadota M, Liu H, Abnet CC, Su H, Wu H, Freedman ND, Yang HH, Wang C, Yan C, Wang L, Gere S, Hutchinson A, Song G, Wang Y, Ding T, Qiao YL, Koshiol J, Dawsey SM, Giffen C, Goldstein AM, Taylor PR, Lee MP. Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer. Cancer Res 2016; 76:1714-23. [PMID: 26857264 DOI: 10.1158/0008-5472.can-15-0338] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023]
Abstract
Gastric cancer and esophageal cancer are the second and sixth leading causes of cancer-related death worldwide. Multiple genomic alterations underlying gastric cancer and esophageal squamous cell carcinoma (ESCC) have been identified, but the full spectrum of genomic structural variations and mutations have yet to be uncovered. Here, we report the results of whole-genome sequencing of 30 samples comprising tumor and blood from 15 patients, four of whom presented with ESCC, seven with gastric cardia adenocarcinoma (GCA), and four with gastric noncardia adenocarcinoma. Analyses revealed that an A>C mutation was common in GCA, and in addition to the preferential nucleotide sequence of A located 5 prime to the mutation as noted in previous studies, we found enrichment of T in the 5 prime base. The A>C mutations in GCA suggested that oxidation of guanine may be a potential mechanism underlying cancer mutagenesis. Furthermore, we identified genes with mutations in gastric cancer and ESCC, including well-known cancer genes, TP53, JAK3, BRCA2, FGF2, FBXW7, MSH3, PTCH, NF1, ERBB2, and CHEK2, and potentially novel cancer-associated genes, KISS1R, AMH, MNX1, WNK2, and PRKRIR Finally, we identified recurrent chromosome alterations in at least 30% of tumors in genes, including MACROD2, FHIT, and PARK2 that were often intragenic deletions. These structural alterations were validated using the The Cancer Genome Atlas dataset. Our studies provide new insights into understanding the genomic landscape, genome instability, and mutation profile underlying gastric cancer and ESCC development. Cancer Res; 76(7); 1714-23. ©2016 AACR.
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Affiliation(s)
- Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Mitsutaka Kadota
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Hailong Wu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Howard H Yang
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Chunhua Yan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sheryl Gere
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland. Cancer Genomics Research Laboratory, Leidos, Gaithersburg, Maryland
| | - Guohong Song
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yuan Wang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, PR China
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, PR China
| | - You-Lin Qiao
- Cancer Institute, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sanford M Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Carol Giffen
- Information Management Services, Inc., Silver Spring, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland.
| | - Maxwell P Lee
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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22
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Moshkovich N, Sato M, Tang B, Yang YA, Flanders KC, Kadota M, Yang H, Lee MP, Wakefield LM. Abstract 2244: Functional interactions between estrogen-related-receptor β (ESRRB) and transforming growth factor-beta (TGF-β) in the regulation of breast cancer stem cell dynamics. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer is a worldwide problem that accounts for almost a quarter of all cancers in women; however, better therapeutic approaches are required since it is estimated that one to three deaths from overtreatment occur for every one death avoided. Our lab is interested in transforming growth factor beta (TGF-β) signaling and its dual role as tumor suppressor/promoter in breast cancer and its therapeutic applications. We previously performed genome-wide ChIP/Chip analysis to identify TGF-β-activated Smad3 target genes in a model of breast cancer progression. We discovered that the estrogen-related-receptor β (ESRRB) transcription factor binding motif was significantly enriched in Smad3 binding regions in breast cancer cell lines. The data suggested that functional interactions between ESRRB and the TGF-β pathway may influence breast cancer progression. ESRRs (α, β, γ) are members of the nuclear orphan receptor family that share significant homology with the estrogen receptors but are not activated by natural estrogens. Additionally, ESRRB maintains pluripotency in embryonic stem cells (ESCs) and is activated by Wnt signaling to promote self-renewal in ESCs. Thus we hypothesized that mechanistically ESRRB/TGF-β may affect breast cancer progression through effects on cancer stem cell (CSC) dynamics and cancer cell differentiation. We showed that ESRRB protein is overexpressed in human breast cancer compared with matched normal breast tissue, and that high expression of ESRRB colocalizes with the stem cell master regulator OCT4 in human breast cancer xenografts. We performed ESRRB knockdown in the MCF10Ca1h, MCF10Ca1a and MDAMB231 breast cancer cell lines and our data demonstrate that ESRRB opposes the inhibitory effects of TGF-β on CSCs as measured by tumorsphere formation assay, while having little or no effect on proliferation of the bulk tumor cell culture in vitro. More importantly, knockdown of ESRRB reduced the in vivo tumorigenicity of all three breast cancer lines and enhanced their histologic differentiation. Extreme limiting dilution assays in vivo showed that knockdown of ESRRB in MDAMB231 cells caused a 78-fold decrease in the relative number of CSCs. In conclusion, our preliminary findings suggest that ESRRB antagonizes the inhibitory effects of TGF-β on CSCs and breast cancer progression, making ESRRB an attractive therapeutic target whose inhibition can restore the tumor suppressive effects of TGF-β and reduce the tumorigenic breast CSC population.
Citation Format: Nellie Moshkovich, Misako Sato, Binwu Tang, Yu-an Yang, Kathleen C. Flanders, Mitsutaka Kadota, Howard Yang, Maxwell P. Lee, Lalage M. Wakefield. Functional interactions between estrogen-related-receptor β (ESRRB) and transforming growth factor-beta (TGF-β) in the regulation of breast cancer stem cell dynamics. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2244. doi:10.1158/1538-7445.AM2015-2244
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23
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Bae E, Sato M, Kim RJ, Kwak MK, Naka K, Gim J, Kadota M, Tang B, Flanders KC, Kim TA, Leem SH, Park T, Liu F, Wakefield LM, Kim SJ, Ooshima A. Definition of smad3 phosphorylation events that affect malignant and metastatic behaviors in breast cancer cells. Cancer Res 2014; 74:6139-49. [PMID: 25205100 DOI: 10.1158/0008-5472.can-14-0803] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Smad3, a major intracellular mediator of TGFβ signaling, functions as both a positive and negative regulator in carcinogenesis. In response to TGFβ, the TGFβ receptor phosphorylates serine residues at the Smad3 C-tail. Cancer cells often contain high levels of the MAPK and CDK activities, which can lead to the Smad3 linker region becoming highly phosphorylated. Here, we report, for the first time, that mutation of the Smad3 linker phosphorylation sites markedly inhibited primary tumor growth, but significantly increased lung metastasis of breast cancer cell lines. In contrast, mutation of the Smad3 C-tail phosphorylation sites had the opposite effect. We show that mutation of the Smad3 linker phosphorylation sites greatly intensifies all TGFβ-induced responses, including growth arrest, apoptosis, reduction in the size of putative cancer stem cell population, epithelial-mesenchymal transition, and invasive activity. Moreover, all TGFβ responses were completely lost on mutation of the Smad3 C-tail phosphorylation sites. Our results demonstrate a critical role of the counterbalance between the Smad3 C-tail and linker phosphorylation in tumorigenesis and metastasis. Our findings have important implications for therapeutic intervention of breast cancer.
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Affiliation(s)
- Eunjin Bae
- CHA Cancer Research Institute, CHA University, Seoul, Korea
| | - Misako Sato
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Ran-Ju Kim
- CHA Cancer Research Institute, CHA University, Seoul, Korea
| | - Mi-Kyung Kwak
- CHA Cancer Research Institute, CHA University, Seoul, Korea
| | - Kazuhito Naka
- Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Jungsoo Gim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Mitsutaka Kadota
- Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Binwu Tang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Kathleen C Flanders
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Tae-Aug Kim
- CHA Cancer Research Institute, CHA University, Seoul, Korea
| | - Sun-Hee Leem
- Department of Biology and Biomedical Science, Dong-A University, Busan, Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea. Department of Statistics, Seoul National University, Seoul, Korea
| | - Fang Liu
- Center for Advanced Biotechnology and Medicine, Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Seong-Jin Kim
- CHA Cancer Research Institute, CHA University, Seoul, Korea.
| | - Akira Ooshima
- CHA Cancer Research Institute, CHA University, Seoul, Korea. Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland.
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Obokata H, Sasai Y, Niwa H, Kadota M, Andrabi M, Takata N, Tokoro M, Terashita Y, Yonemura S, Vacanti CA, Wakayama T. Retraction: Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature 2014; 511:112. [PMID: 24990752 DOI: 10.1038/nature13599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Sato M, Kadota M, Tang B, Yang HH, Yang YA, Shan M, Weng J, Welsh MA, Flanders KC, Nagano Y, Michalowski AM, Clifford RJ, Lee MP, Wakefield LM. An integrated genomic approach identifies persistent tumor suppressive effects of transforming growth factor-β in human breast cancer. Breast Cancer Res 2014; 16:R57. [PMID: 24890385 PMCID: PMC4095608 DOI: 10.1186/bcr3668] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/21/2014] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Transforming growth factor-βs (TGF-βs) play a dual role in breast cancer, with context-dependent tumor-suppressive or pro-oncogenic effects. TGF-β antagonists are showing promise in early-phase clinical oncology trials to neutralize the pro-oncogenic effects. However, there is currently no way to determine whether the tumor-suppressive effects of TGF-β are still active in human breast tumors at the time of surgery and treatment, a situation that could lead to adverse therapeutic responses. METHODS Using a breast cancer progression model that exemplifies the dual role of TGF-β, promoter-wide chromatin immunoprecipitation and transcriptomic approaches were applied to identify a core set of TGF-β-regulated genes that specifically reflect only the tumor-suppressor arm of the pathway. The clinical significance of this signature and the underlying biology were investigated using bioinformatic analyses in clinical breast cancer datasets, and knockdown validation approaches in tumor xenografts. RESULTS TGF-β-driven tumor suppression was highly dependent on Smad3, and Smad3 target genes that were specifically enriched for involvement in tumor suppression were identified. Patterns of Smad3 binding reflected the preexisting active chromatin landscape, and target genes were frequently regulated in opposite directions in vitro and in vivo, highlighting the strong contextuality of TGF-β action. An in vivo-weighted TGF-β/Smad3 tumor-suppressor signature was associated with good outcome in estrogen receptor-positive breast cancer cohorts. TGF-β/Smad3 effects on cell proliferation, differentiation and ephrin signaling contributed to the observed tumor suppression. CONCLUSIONS Tumor-suppressive effects of TGF-β persist in some breast cancer patients at the time of surgery and affect clinical outcome. Carefully tailored in vitro/in vivo genomic approaches can identify such patients for exclusion from treatment with TGF-β antagonists.
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Affiliation(s)
- Misako Sato
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
- Department of Hepatology, Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno, Osaka 545-8585, Japan
| | - Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
- Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minami-machi, Chuo-ku Kobe, Hyogo 650-0047, Japan
| | - Binwu Tang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Howard H Yang
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
| | - Yu-an Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Mengge Shan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Jia Weng
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Michael A Welsh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Kathleen C Flanders
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Yoshiko Nagano
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
- Department of Immunotherapeutics, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Aleksandra M Michalowski
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Robert J Clifford
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring MD 2091, 0USA
| | - Maxwell P Lee
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA
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Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR, Niwa H. Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells. Mol Cell 2013; 52:380-92. [PMID: 24120664 DOI: 10.1016/j.molcel.2013.09.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 07/08/2013] [Accepted: 08/29/2013] [Indexed: 01/03/2023]
Abstract
Sox2 is a transcription factor required for the maintenance of pluripotency. It also plays an essential role in different types of multipotent stem cells, raising the possibility that Sox2 governs the common stemness phenotype. Here we show that Sox2 is a critical downstream target of fibroblast growth factor (FGF) signaling, which mediates self-renewal of trophoblast stem cells (TSCs). Sustained expression of Sox2 together with Esrrb or Tfap2c can replace FGF dependency. By comparing genome-wide binding sites of Sox2 in embryonic stem cells (ESCs) and TSCs combined with inducible knockout systems, we found that, despite the common role in safeguarding the stem cell state, Sox2 regulates distinct sets of genes with unique functions in these two different yet developmentally related types of stem cells. Our findings provide insights into the functional versatility of transcription factors during embryogenesis, during which they can be recursively utilized in a variable manner within discrete network structures.
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Affiliation(s)
- Kenjiro Adachi
- Laboratory for Pluripotent Stem Cell Studies, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 6500047, Japan.
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Sato M, Kadota M, Tang B, Yang YA, Shan M, Weng J, Welsh M, Nagano Y, Michalowski A, Yang H, Clifford R, Lee M, Wakefield L. Abstract B029: Dissecting out the tumor suppressor aspect of TGF-β in breast cancer using integrated genomics. Mol Cancer Res 2013. [DOI: 10.1158/1557-3125.advbc-b029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The purpose of our study was to identify a gene expression signature that specifically reflects the tumor suppressive effects of transforming growth factor-β (TGF-β), for use as a negative selective biomarker in clinical trials using TGF-β antagonists. TGF-β effects are highly contextual, and the dogma is that tumor suppressive effects are active in the early stages of carcinogenesis, but that pro-progression effects come to dominate later on. Since TGF-β antagonists are in early phase clinical trials in cancer, it is important to know whether the tumor suppressive effects of TGF-β are still intact in any tumors at the time of diagnosis and treatment, as this would be a contraindication for anti-TGF-β therapy. Existing TGF-β-related gene expression signatures were not designed a priori to discriminate the tumor suppressive from the tumor promoting activities. To address this question, we applied integrated ChIP-chip and transcriptomic approaches in the MCF10A-based model of breast cancer progression. We have previously shown that TGF-β has tumor suppressor activity in the less malignant cell lines of the series (MCF10AT1k, MCF10Ca1h), but that this effect is lost in the most malignant cell line (MCF10Ca1a). Here we showed that the tumor suppressor activity in this model system is specifically dependent on the downstream signaling component Smad3 and not Smad2. Using promoter-wide ChIP-chip, we found that the genomic landscape of TGF-β induced Smad3 binding differed dramatically between the four cell lines, despite their close genetic relatedness and similar Smad3 levels and activation profiles. Interestingly, TGF-β induced Smad3 binding only at loci that were already transcriptionally active, suggesting that TGF-βs may primarily play a modulator rather than an instigator role in regulating transcription. This feature probably contributes importantly to the known contextuality of TGF-β activity. By focusing on the two malignant cell lines (MCF10CA1h and MCF10CA1a), we identified a core signature of 26 TGF-β/Smad3 regulated genes that was specifically associated with the tumor suppressor activity of TGF-β. Unexpectedly, the direction of regulation of 25% of these genes by TGF-β differed in vitro and in vivo, highlighting a further novel contribution to TGF-β contextuality. The in vivo weighted form of the TGF-β/Smad3 tumor suppressor signature (TSTSS) was associated with good outcome specifically in estrogen-receptor positive (ER+) breast cancer patients, suggesting that TGF-β tumor suppressive pathways are still active and influencing disease outcome in a subset of patients at the time of surgery. TGF-β is a potent growth inhibitor for most epithelial cells and the TSTSS was weakly inversely correlated with proliferation in ER+ breast cancer, but the signature prognosticated independently of proliferation in multivariate analysis. Instead, the TSTSS was enriched for genes involved in cellular differentiation and movement, and ephrin was the top enriched signaling pathway. Ephrin knockdown in MCF10Ca1h cells led to increased migration, reduced apoptosis and differentiation and enhanced tumorigenesis. Our demonstration that a subset of breast cancer patients still has an active TGF-β tumor suppressor pathway at the time of surgery has important implications for patient stratification in ongoing clinical trials with TGF-β antagonists.
Citation Format: Misako Sato, Mitsutaka Kadota, Binwu Tang, Yu-an Yang, Mengge Shan, Jia Weng, Michael Welsh, Yoshiko Nagano, Aleksandra Michalowski, Howard Yang, Robert Clifford, Maxwell Lee, Lalage Wakefield. Dissecting out the tumor suppressor aspect of TGF-β in breast cancer using integrated genomics. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B029.
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Affiliation(s)
| | | | | | | | | | - Jia Weng
- National Cancer Institute, Bethesda, MD
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Sato M, Kadota M, Tang B, Yang YA, Shan M, Weng J, Welsh M, Michalowski A, Yang H, Clifford R, Lee M, Wakefield LM. Abstract 4310: An integrated genomic approach specifically dissects out the tumor suppressor aspect of TGF-β in breast cancer. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Transforming growth factor-βs (TGF-βs) have complex roles in tumorigenesis, with context-dependent effects that can either suppress or promote tumor progression. The dogma is that tumor suppressive effects are active in the early stages of carcinogenesis, but that later pro-progression effects come to dominate. Since TGF-β antagonists of various types are in early phase clinical trials in cancer, it is important to know whether the tumor suppressive effects of TGF-β are still intact in any tumors at the time of diagnosis and treatment. Existing TGF-β-related gene expression signatures were not designed a priori to discriminate the tumor suppressive from the tumor promoting activities. To address this question, we applied integrated ChIP-chip and transcriptomic approaches in the MCF10A-based model of breast cancer progression. We have previously shown that TGF-β has tumor suppressor activity in the less malignant cell lines of the series (MCF10A, MCF10AT1k, MCF10Ca1h), but that this effect is lost in the most malignant cell line (MCF10Ca1a). The tumor suppressor activity is dependent on the downstream signaling component Smad3. Using promoter-wide ChIP-chip, we found that the genomic landscape of TGF-β induced Smad3 binding differed dramatically between the four cell lines, despite their close genetic relatedness. Interestingly, TGF-β induced Smad3 binding only at genetic loci that were already transcriptionally active, suggesting that TGF-βs may primarily play a modulator rather than an instigator role in regulating transcription. This feature probably contributes significantly to the known contextuality of TGF-β activity. By focusing on the two malignant cell lines (MCF10CA1h and MCF10CA1a), we identified a core signature of 26 TGF-β/Smad3 regulated genes that were specifically associated with the tumor suppressor activity of TGF-β. Unexpectedly, the direction of regulation of 25% of these genes by TGF-β differed in vitro and in vivo, highlighting a further novel contribution to TGF-β contextuality, and emphasizing the importance of including in vivo data in this type of analysis. The in vivo weighted form of the TGF-β/Smad3 tumor suppressor signature was associated with good outcome in estrogen-receptor positive breast cancer patients, suggesting that TGF-β tumor suppressive pathways are still active and influencing disease outcome in a subset of patients’ tumors at the time of surgery. TGF-β is a potent growth inhibitor for most epithelial cells, but anti-proliferative effects made only a minor contribution to the tumor suppressor activity in the breast cancer cohorts. Instead, novel tumor suppressor effects of TGF-β captured by this approach included the restoration of tumor suppressive EphrinA signaling, leading to increased tumor cell differentiation. The results have important implications for patient stratification in ongoing clinical trials with TGF-β antagonists.
Citation Format: Misako Sato, Mitsutaka Kadota, Binwu Tang, Yu-an Yang, Mengge Shan, Jia Weng, Michael Welsh, Aleksandra Michalowski, Howard Yang, Robert Clifford, Maxwell Lee, Lalage M. Wakefield. An integrated genomic approach specifically dissects out the tumor suppressor aspect of TGF-β in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4310. doi:10.1158/1538-7445.AM2013-4310
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Affiliation(s)
| | | | | | | | | | - Jia Weng
- National Cancer Inst., Bethesda, MD
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Tanaka M, Miyazawa K, Tabuchi M, Yabumoto T, Kadota M, Yoshizako M, Yamane C, Kawatani M, Osada H, Maeda H, Goto S. Effect of Reveromycin A on experimental tooth movement in OPG-/- mice. J Dent Res 2012; 91:771-6. [PMID: 22674934 DOI: 10.1177/0022034512451026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
In osteoprotegerin-deficient (OPG-/-) mice, osteoclast activity causes bone resorption to outpace bone formation, leading to the development of severe osteoporosis. Such mice are therefore useful for investigating the alveolar bone of patients with osteoporosis. Reveromycin A (RM-A) was recently identified as the unique agent acting on osteoclast activation. This study aimed to analyze the effect of RM-A on the orthodontic treatment of OPG-/- mice (a model of osteoporosis patients with high levels of bone turnover). We examined alveolar bone remodeling in OPG-/- and wild-type (WT) mice during continuous tooth movement. The orthodontic force was induced by means of a Ni-Ti closed-coil spring to move the maxillary first molar for 14 days. RM-A sodium salt (1 mg/kg) was administered intraperitoneally twice daily. In OPG-/- mice, the tooth movement distance was longer, alveolar bone resorption was enhanced, the osteoclast count was greater, and serum alkaline phosphatase and tartrate-resistant acid phosphatase levels were higher relative to those in WT mice. However, the administration of RM-A in OPG-/- mice reduced these parameters. We conclude that RM-A normalizes bone metabolism and loss of alveolar bone during continuous tooth movement in OPG-/- mice.
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Affiliation(s)
- M Tanaka
- Department of Orthodontics, School of Dentistry, Aichi-Gakuin University, Chikusa-ku, Nagoya, Japan.
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Lee MP, Kadota M. Abstract 4971: Transcriptome analysis and the identification of novel somatic mutations in breast cancer by the next-generation sequencing. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Breast cancer is the most common cancer among women in the United States and the second most common cause of cancer mortality in this population. Despite extensive research, the complexity of this disease has caused it to elude simple approaches to prevention and treatment. Breast cancer is a collection of heterogeneous tumor types that exhibit distinct histopathological features. This has clinical implications since these breast cancer types often correlate with patient outcomes such as prognosis, response to treatment, and survival. In this study, we present a comprehensive characterization of transcriptomes for breast tumors and their adjacent normal tissues using the next-generation sequencing (NGS) technology.
Material and Methods: We analyzed 8 samples: 4 primary breast tumors (2 triple negatives; 2 HER2 positive and ER/PR negative) and 4 matched normal tissues. Poly-A mRNA was isolated and sequenced using Illumina GAII. We obtained about 140 millions of 76 bp pair-end reads for each sample. The sequences were mapped to the hg18 reference sequences with BWA, and the mapping efficiency of our data was around 90%. Validation of mutations was performed using the traditional ABI sequencing.
Results and Discussion: We compared gene expression difference between tumor and its matched adjacent normal tissue and found that a large number of genes showed significant changes in expression level (FDR=0.1), including more than 10,000 down-regulated genes and around 4,000 up-regulated genes. Examples of down-regulated genes include GNAS, TP73L, and KRT14 whereas up-regulated genes include TOP2A, MMP9, and FOXM1. Nucleotide-resolution of the NGS data made it possible to identify changes in specific isoforms for each gene. As an example, GNAS is a complex locus, containing 7 Refseq transcripts, 3 of which are subject to genomic imprinting regulation (one expressed from the maternal chromosome and two from the paternal chromosome) and the other 4 transcripts are normally expressed from both chromosomes; down-regulation of GNAS affected only the maternally expressed imprinted transcript whereas bi-allelic transcripts were expressed at high-level in both tumors and normal tissues. Furthermore, the NGS data also enabled us to identify somatic mutations. We uncovered 28 sequence variants that changed coding sequences and were mutated specifically in tumors. We were able to design PCR primers for 22 variants for analysis by the use of traditional ABI sequencing. We validated 14 out of 22 mutations, one of which is a known mutation, G1049R, in the PIK3CA gene and the other 13 are novel mutations, including mutations in ARID1B and VIM. In conclusion, our NGS analysis of breast cancer transcriptomes has generated new insights into both transcription regulation and genetic alterations, and these new insights may be explored for better diagnosis and treatment of breast cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4971. doi:10.1158/1538-7445.AM2011-4971
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Lee MP, Kadota M, Yang HH, Clifford RJ, Dunn BK. Abstract P3-04-04: Novel Genome-Wide DNA Methylation Signatures of Primary Breast Tumor Subtypes. Cancer Res 2010. [DOI: 10.1158/0008-5472.sabcs10-p3-04-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Gene expression signatures can be used to classify breast tumor tissues into distinct categories: luminal, “basal”, and HER2 subtypes, which have distinct clinical prognoses. Since gene expression is largely determined at the level of epigenetic modification, we hypothesize that DNA methylation signatures may also be used to classify breast tumor subtypes and possibly to define new cancer subtypes; thus, such epigenetic signatures can complement gene expression signatures for a better understanding of breast tumorigenesis and in turn, may lead to improvement in clinical diagnosis.
Material and Methods: We used antibodies to 5-methylcytosine to immunoprecipitate DNA enriched for methylation by means of the MeDIP method on 66 breast primary tumors. Then we analyzed the MeDIP-derived DNA by means of the Affymetrix 500K SNP array. We normalized DNA methylation data from the 66 tumors using a modified quantile normalization procedure. The data were generated in two phases, phase 1 consisting of 42 tumors and phase 2 containing 24 tumors, data from the latter being reserved for validation purposes. We concentrated DNA methylation analysis on the SNPs that are located within promoter regions, defined here as +/− 2 kb flanking the transcription start site (TSS), and within CpG islands, since methylation in these regions is especially relevant for gene expression regulation. We searched for DNA methylation signatures that show distinct patterns among tumors with different clinical phenotypes such as histological grade and lymph node involvement. Results: We identified one DNA methylation signature consists of 78 genes that separated the tumors with high grade from those with low-mid grade; we found another DNA methylation signature consists of 42 genes that separated the tumors with lymph node positive status from those with lymph node negative status. We were able to validate these signatures using methylation data obtained from an independent set of 24 tumors. The performance of the signature for predicting lymph node status in the testing samples showed accuracy of 83%, sensitivity of 70%, and specificity of 90%.
Discussion: We have identified DNA methylation signatures that could classify breast tumor subtypes and correlate with clinical phenotypes. We are investigating whether such epigenetic signatures can complement gene expression signatures for a better understanding of breast tumorigenesis and for application in clinical diagnosis and treatment.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-04-04.
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Affiliation(s)
- MP Lee
- National Cancer Institute, Bethesda, MD
| | - M Kadota
- National Cancer Institute, Bethesda, MD
| | - HH Yang
- National Cancer Institute, Bethesda, MD
| | | | - BK. Dunn
- National Cancer Institute, Bethesda, MD
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Kadota M, Yang HH, Gomez B, Sato M, Clifford RJ, Meerzaman D, Dunn BK, Wakefield LM, Lee MP. Delineating genetic alterations for tumor progression in the MCF10A series of breast cancer cell lines. PLoS One 2010; 5:e9201. [PMID: 20169162 PMCID: PMC2821407 DOI: 10.1371/journal.pone.0009201] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 01/26/2010] [Indexed: 01/22/2023] Open
Abstract
To gain insight into the role of genomic alterations in breast cancer progression, we conducted a comprehensive genetic characterization of a series of four cell lines derived from MCF10A. MCF10A is an immortalized mammary epithelial cell line (MEC); MCF10AT is a premalignant cell line generated from MCF10A by transformation with an activated HRAS gene; MCF10CA1h and MCF10CA1a, both derived from MCF10AT xenografts, form well-differentiated and poorly-differentiated malignant tumors in the xenograft models, respectively. We analyzed DNA copy number variation using the Affymetrix 500 K SNP arrays with the goal of identifying gene-specific amplification and deletion events. In addition to a previously noted deletion in the CDKN2A locus, our studies identified MYC amplification in all four cell lines. Additionally, we found intragenic deletions in several genes, including LRP1B in MCF10CA1h and MCF10CA1a, FHIT and CDH13 in MCF10CA1h, and RUNX1 in MCF10CA1a. We confirmed the deletion of RUNX1 in MCF10CA1a by DNA and RNA analyses, as well as the absence of the RUNX1 protein in that cell line. Furthermore, we found that RUNX1 expression was reduced in high-grade primary breast tumors compared to low/mid-grade tumors. Mutational analysis identified an activating PIK3CA mutation, H1047R, in MCF10CA1h and MCF10CA1a, which correlates with an increase of AKT1 phosphorylation at Ser473 and Thr308. Furthermore, we showed increased expression levels for genes located in the genomic regions with copy number gain. Thus, our genetic analyses have uncovered sequential molecular events that delineate breast tumor progression. These events include CDKN2A deletion and MYC amplification in immortalization, HRAS activation in transformation, PIK3CA activation in the formation of malignant tumors, and RUNX1 deletion associated with poorly-differentiated malignant tumors.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
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Kadota M, Sato M, Duncan B, Ooshima A, Yang HH, Diaz-Meyer N, Gere S, Kageyama SI, Fukuoka J, Nagata T, Tsukada K, Dunn BK, Wakefield LM, Lee MP. Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA. Cancer Res 2009; 69:7357-65. [PMID: 19706770 DOI: 10.1158/0008-5472.can-09-0064] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To identify genetic events that characterize cancer progression, we conducted a comprehensive genetic evaluation of 161 primary breast tumors. Similar to the "mountain-and-hill" view of mutations, gene amplification also shows high- and low-frequency alterations in breast cancers. The frequently amplified genes include the well-known oncogenes ERBB2, FGFR1, MYC, CCND1, and PIK3CA, whereas other known oncogenes that are amplified, although less frequently, include CCND2, EGFR, FGFR2, and NOTCH3. More importantly, by honing in on minimally amplified regions containing three or fewer genes, we identified six new amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4. We found that both the IRX2 and TBL1XR1 proteins showed higher expression in the malignant cell lines MCF10CA1h and MCF10CA1a than in their precursor, MCF10A, a normal immortalized mammary epithelial cell line. To study oncogenic roles of TBL1XR1, we performed knockdown experiments using a short hairpin RNA approach and found that depletion of TBL1XR1 in MCF10CA1h cells resulted in reduction of cell migration and invasion as well as suppression of tumorigenesis in mouse xenografts. Intriguingly, our mutation analysis showed the presence of activation mutations in the PIK3CA gene in a subset of tumors that also had DNA copy number increases in the PIK3CA locus, suggesting an additive effect of coexisting activating amino acid substitution and dosage increase from amplification. Our gene amplification and somatic mutation analysis of breast primary tumors provides a coherent picture of genetic events, both corroborating and novel, offering insight into the genetic underpinnings of breast cancer progression.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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Ueno S, Shibata K, Kitai R, Ichimoto K, Nagata S, Isobe H, Kimura G, Nakatani Y, Kadota M, Ishii TT, Morita S, Otsuji K. The CHAIN-Project and Installation of Flare Monitoring Telescopes in Developing Countries. Data Sci J 2009. [DOI: 10.2481/dsj.8.s51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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35
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Kadota M, Yang HH, Hu N, Wang C, Hu Y, Taylor PR, Buetow KH, Lee MP. Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome. PLoS Genet 2007; 3:e81. [PMID: 17511522 PMCID: PMC1868950 DOI: 10.1371/journal.pgen.0030081] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 04/06/2007] [Indexed: 11/19/2022] Open
Abstract
Several recent studies have shown a genetic influence on gene expression variation, including variation between the two chromosomes within an individual and variation between individuals at the population level. We hypothesized that genetic inheritance may also affect variation in chromatin states. To test this hypothesis, we analyzed chromatin states in 12 lymphoblastoid cells derived from two Centre d'Etude du Polymorphisme Humain families using an allele-specific chromatin immunoprecipitation (ChIP-on-chip) assay with Affymetrix 10K SNP chip. We performed the allele-specific ChIP-on-chip assays for the 12 lymphoblastoid cells using antibodies targeting at RNA polymerase II and five post-translation modified forms of the histone H3 protein. The use of multiple cell lines from the Centre d'Etude du Polymorphisme Humain families allowed us to evaluate variation of chromatin states across pedigrees. These studies demonstrated that chromatin state clustered by family. Our results support the idea that genetic inheritance can determine the epigenetic state of the chromatin as shown previously in model organisms. To our knowledge, this is the first demonstration in humans that genetics may be an important factor that influences global chromatin state mediated by histone modification, the hallmark of the epigenetic phenomena. Human health and disease are determined by an interaction between genetic background and environmental exposures. Both normal development and disease are mediated by epigenetic regulation of gene expression. The epigenetic regulation causes heritable changes in gene expression, which is not associated with DNA sequence changes. Instead, it is mediated by chemical modification of DNA such as DNA methylation or by protein modifications such as histone acetylation and methylation. Although much has been known about epigenetic inheritance during development, little is known about the influence of the genetic background on epigenetic processes such as histone modifications. In this report the authors studied five histone modifications on a genome-wide level in cells from different families. Global epigenetic states, as measured by these histone modifications, showed a similar pattern for cells derived from the same family. This study demonstrates that genetic inheritance may be an important factor influencing global chromatin states mediated by histone modifications in humans. These observations illustrate the importance of integrating genetic and epigenetic information into studies of human health and complex diseases.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Howard H Yang
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nan Hu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chaoyu Wang
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ying Hu
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Philip R Taylor
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kenneth H Buetow
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maxwell P Lee
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Torisu H, Yamamoto T, Fujiwaki T, Kadota M, Oshimura M, Kurosawa K, Akaboshi S, Oka A. Girl with monosomy 1p36 and Angelman syndrome due to unbalanced der(1) transmission of a maternal translocation t(1;15)(p36.3;q13.1). ACTA ACUST UNITED AC 2004; 131:94-8. [PMID: 15384094 DOI: 10.1002/ajmg.a.30413] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report on a girl with monosomy 1p36.3 and Angelman syndrome due to an unbalanced transmission of a maternal balanced chromosomal translocation. She manifested monosomy 1p36 and Angelman syndrome including generalized hypopigmentation, ataxic movements, intractable seizures with characteristic electroencephalographic (EEG) abnormality compatible with Angelman syndrome, and other minor anomalies, large anterior fontanelle, severe psychomotor retardation, and seizures due to monosomy 1p36. Her karyotype was 45, XX, der(1) t(1;15)(p36.31;q13.1),-15, derived from maternal translocation. Molecular analysis determined a breakpoint of 1p between D1S243 and D1S468, which suggested that most genes contributing to the common phenotype are in the distal region.
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Affiliation(s)
- Hiroyuki Torisu
- Division of Child Neurology, Institute of Neurological Sciences, Faculty of Medicine, Tottori University, Yonago, Japan.
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Murakami K, Nishigaki R, Kazuki Y, Kadota M, Oshimura M. [Proteomics and epigenetics learned from Down syndrome model mouse]. Seikagaku 2004; 76:1296-304. [PMID: 15580861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- Kaori Murakami
- Department of Human Genome Science, Molecular and Cell Genetics, Graduate School of Medical Science, Tottori University, 86 Nishimachi, Yonago, Tottori 683-8503, Japan
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Kazuki Y, Schulz TC, Shinohara T, Kadota M, Nishigaki R, Inoue T, Kimura M, Kai Y, Abe S, Shirayoshi Y, Oshimura M. A new mouse model for Down syndrome. ACTA ACUST UNITED AC 2004:1-20. [PMID: 15068235 DOI: 10.1007/978-3-7091-6721-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Trisomy 21 (Ts21) is the most common live-born human aneuploidy and results in a constellation of features known as Down syndrome (DS). Ts21 is a frequent cause of congenital heart defects and the leading genetic cause of mental retardation. Although overexpression of a gene(s) or gene cluster on human chromosome 21 (Chr 21) or the genome imbalance by Ts21 has been suggested to play a key role in bringing about the diverse DS phenotypes, little is known about the molecular mechanisms underlying the various phenotypes associated with DS. Four approaches have been used to model DS to investigate the gene dosage effects of an extra copy of Chr 21 on various phenotypes; 1) Transgenic mice overexpressing a single gene from Chr 21, 2) YAC/BAC/PAC transgenic mice containing a single gene or genes on Chr 21, 3) Mice with intact/partial trisomy 16, a region with homology to human Chr 21 and 4) Human Chr 21 transchromosomal (Tc) mice. Here we review our new model system for the study of DS using the Tc technology, including the biological effects of an additional Chr 21 in vivo and in vitro.
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Affiliation(s)
- Y Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medicine, Tottori University, Yonago, Tottori, Japan
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Wang CC, Kadota M, Nishigaki R, Kazuki Y, Shirayoshi Y, Rogers MS, Gojobori T, Ikeo K, Oshimura M. Molecular hierarchy in neurons differentiated from mouse ES cells containing a single human chromosome 21. Biochem Biophys Res Commun 2004; 314:335-50. [PMID: 14733910 DOI: 10.1016/j.bbrc.2003.12.091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Defects in neurogenesis and neuronal differentiation in the fetal brain of Down syndrome (DS) patients lead to the apparent neuropathological abnormalities and contribute to the phenotypic characters of mental retardation, and premature development of Alzheimer's disease, those being the most common phenotype in DS. In order to understand the molecular mechanism underlying the cause of phenotypic abnormalities in the DS brain, we have utilized an in vitro model of TT2F mouse embryonic stem cells containing a single human chromosome 21 (hChr21) to study neuron development and neuronal differentiation by microarray containing 15K developmentally expressed cDNAs. Defective neuronal differentiation in the presence of extra hChr21 manifested primarily the post-transcriptional and translational modification, such as Mrpl10, SNAPC3, Srprb, SF3a60 in the early neuronal stem cell stage, and Mrps18a, Eef1g, and Ubce8 in the late differentiated stage. Hierarchical clustering patterned specific expression of hChr21 gene dosage effects on neuron outgrowth, migration, and differentiation, such as Syngr2, Dncic2, Eif3sf, and Peg3.
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Affiliation(s)
- Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong
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40
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Kadota M, Nishigaki R, Wang CC, Toda T, Shirayoshi Y, Inoue T, Gojobori T, Ikeo K, Rogers MS, Oshimura M. Proteomic signatures and aberrations of mouse embryonic stem cells containing a single human chromosome 21 in neuronal differentiation: An in vitro model of down syndrome. Neuroscience 2004; 129:325-35. [PMID: 15501590 DOI: 10.1016/j.neuroscience.2004.06.081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2004] [Indexed: 11/16/2022]
Abstract
Neurodegeneration in fetal development of Down syndrome (DS) patients is proposed to result in apparent neuropathological abnormalities and to contribute to the phenotypic characteristics of mental retardation and premature development of Alzheimer disease. In order to identify the aberrant and specific genes involved in the early differentiation of DS neurons, we have utilized an in vitro neuronal differentiation system of mouse ES cells containing a single human chromosome 21 (TT2F/hChr21) with TT2F parental ES cells as a control. The paired protein extracts from TT2F and TT2F/hChr21 cells at several stages of neuronal differentiation were subjected to two-dimensional polyacrylamide gel electrophoresis protein separation followed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry to identify the proteins differentially expressed between TT2F and TT2F/hChr21 cells. We provide here a novel set of specific gene products altered in early differentiating DS neuronal cells, which differs from that identified in adult or fetal brain with DS. The aberrant protein expression in early differentiating neurons, due to the hChr21 gene dosage effects or chromosomal imbalance, may affect neuronal outgrowth, proliferation and differentiation, producing developmental abnormalities in neural patterning, which eventually leads to formation of a suboptimal functioning neuronal network in DS.
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Affiliation(s)
- M Kadota
- Department of Human Genome Science (Kirin Brewery), Graduate School of Medical Science, Tottori University, 86 Nishimachi, Yonago, Tottori 683-8503, Japan
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Hamada Y, Kawachi K, Tsunooka N, Nakamura Y, Takano S, Imagawa H, Kadota M. [Assessment of extracellular fluid in cardiac surgery using cardiopulmonary bypass]. Kyobu Geka 2003; 56:1011-3. [PMID: 14608923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Extracellular fluid (ECF) was assessed before and after the cardiac surgery using cardiopulmonary bypass (CPB), by means of a bioimpedance spectrum analyzer to see volumes of the fluid based on changes of the impedance to various frequencies. Difference between the levels before and after the operation was divided by body weight to study about a % BW. Simultaneously its relation to the lung compliance [tidal volume/(peak inspiratory pressure-end expiratory pressure)] was studied. Mean age of the 18 patients was 59.1 +/- 19 years old. ECF was assessed before to 24 hours after the operation continuously and once more after 48 hours. Mean CPB time was 165 +/- 52 minutes, and aortic cross clamp time was 121 +/- 4 minutes. A remarkable increase of ECF was noted immediately after the operation, which further increased gradually till arriving at the peak 4 hours after the operation (4.52 +/- 1.8% BW). Then it gradually decreased to 0.641 +/- 2.7% BW 48 hours later. Lung compliance measured at the same time showed the lowest level 6 hours after the operation. It was known that the bioimpedance spectrum analysis is a simple and non-invasive method, which enables to monitor the vital stable before and after the operation.
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Affiliation(s)
- Yoshihiro Hamada
- Department of Second Surgery, Ehime University School of Medicine, Ehime, Japan
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Fujii S, Luo RZ, Yuan J, Kadota M, Oshimura M, Dent SR, Kondo Y, Issa JPJ, Bast RC, Yu Y. Reactivation of the silenced and imprinted alleles of ARHI is associated with increased histone H3 acetylation and decreased histone H3 lysine 9 methylation. Hum Mol Genet 2003; 12:1791-800. [PMID: 12874100 DOI: 10.1093/hmg/ddg204] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
ARHI has been identified as a maternally imprinted tumor suppressor gene that maps to chromosome 1p31 and whose expression is markedly down-regulated in breast cancer. To explore possible mechanisms that could silence ARHI expression, we have tested the importance of DNA methylation, histone acetylation and histone methylation in regulating ARHI expression. We found that treatment with CpG demethylating agents and/or histone deacetylase inhibitors could reactivate both the silenced and the imprinted alleles of this tumor suppressor gene. Reactivation of ARHI expression by these reagents is related to the methylation status of the CpG islands in the ARHI promoter, especially CpG island II. Chromatin immunoprecipitation assays revealed that histone H3 lysine 9/18 acetylation levels associated with ARHI in normal cells were significantly higher than those in breast cancer cell lines that lacked ARHI expression. Treatment with a CpG demethylating agent and/or histone deacetylase inhibitor could increase ARHI expression in breast cancer cells, with a corresponding increase in histone H3 lysine 9/18 acetylation and decrease in histone H3 lysine 9 methylation.
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Affiliation(s)
- Satoshi Fujii
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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Yuan J, Luo RZ, Fujii S, Wang L, Hu W, Andreeff M, Pan Y, Kadota M, Oshimura M, Sahin AA, Issa JP, Bast RC, Yu Y. Aberrant methylation and silencing of ARHI, an imprinted tumor suppressor gene in which the function is lost in breast cancers. Cancer Res 2003; 63:4174-80. [PMID: 12874023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
ARHI is a maternally imprinted tumor suppressor gene that maps to a site on chromosome 1p31 where loss of heterozygosity has been observed in 40% of human breast and ovarian cancers. ARHI is expressed in normal ovarian and breast epithelial cells, but ARHI expression is lost in a majority of ovarian and breast cancers. Expression of ARHI from the paternal allele can be down-regulated by multiple mechanisms in addition to loss of heterozygosity. This article explores the role of DNA methylation in silencing ARHI expression. There are three CpG islands in the ARHI gene. CpG islands I and II are located in the promoter region, whereas CpG island III is located in the coding region. Consistent with imprinting, we have found that all three CpG islands were partially methylated in normal human breast epithelial cells. Additional confirmation of imprinting has been obtained by studying DNA methylation and ARHI expression in murine A9 cells that carry either the maternal or the paternal copy of human chromosome 1. All three CpG islands were methylated, and ARHI was not expressed in A9 cells that contained the maternal allele. Conversely, CpG islands were not methylated and ARHI was expressed in A9 cells that contained the paternal allele of human chromosome 1. Aberrant methylation was found in several breast cancer cell lines that exhibited decreased ARHI expression. Hypermethylation was detected in 67% (6 of 9) of breast cancer cell lines at CpG island I, 33% (3 of 9) at CpG island II, and 56% (5 of 9) at CpG island III. Hypomethylation was observed in 44% (4 of 9) of breast cancer cell lines at CpG island II. When methylation of CpG islands was studied in 20 surgical specimens, hypermethylation was not observed in CpG island I, but 3 of 20 cases exhibited hypermethylation in CpG island II (15%), and 4 of 20 cases had hypermethylation in CpG island III (20%). Treatment with 5-aza-2'-deoxycytidine, a methyltransferase inhibitor, could reverse aberrant hypermethylation of CpG island I, II and III and partially restore ARHI expression in some, but not all of the cell lines. Treatment with 5-aza-2'-deoxycytidine partially reactivated ARHI expression in cell lines with hypermethylation of CpG islands I and II but not in cell lines with partial methylation or hypomethylation of these CpG islands. To test the impact of CpG island methylation on ARHI promoter activity more directly, constructs were prepared with the ARHI promoter linked to a luciferase reporter and transfected into SKBr3 and human embryo kidney 293 cells. Methylation of the entire construct destroyed promoter activity. Selective methylation of CpG island II alone or in combination with CpG island I also abolished ARHI promoter activity. Methylation of CpG I alone partially inhibited promoter activity of ARHI. Thus, hypermethylation of CpG island II in the promoter region of ARHI is associated with the complete loss of ARHI expression in breast cancer cells. Other epigenetic modifications such as hypermethylation in CpG island III may also contribute to the loss of ARHI expression.
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Affiliation(s)
- Jiuhong Yuan
- Department of Experimental Therapeutics, The University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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Yu Y, Fujii S, Yuan J, Luo RZ, Wang L, Bao J, Kadota M, Oshimura M, Dent SR, Issa JP, Bast RC. Epigenetic regulation of ARHI in breast and ovarian cancer cells. Ann N Y Acad Sci 2003; 983:268-77. [PMID: 12724231 DOI: 10.1111/j.1749-6632.2003.tb05981.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
ARHI (Ras homologue member I) encodes a 26-kDa GTPase with 50-60% amino acid homology to Ras and Rap. ARHI and Ras share similar GTP/GDP binding domains, but exert opposite functions. ARHI is one of the first reported tumor suppressors in the ras superfamily. ARHI is expressed consistently in normal breast and ovarian epithelial cells, but not in breast or ovarian cancers. The loss of ARHI can be related to tumor progression. Reexpression of ARHI induces apoptosis of breast and ovarian cancer cells by a caspase-independent, calpain-dependent pathway. ARHI is consistently expressed in normal breast and ovarian epithelial cells but is dramatically downregulated in more then 70% of breast and ovarian cancers. ARHI is maternally imprinted with methylation of the three CpG islands in the maternal allele of normal cells. ARHI is expressed only from the paternal allele whose three CpG islands are not methylated. Loss of ARHI expression can occur through a genetic event, with loss of heterozygosity observed in 40% of breast, ovarian, and pancreatic cancers; but it can also occur through epigenetic mechanisms, including DNA methylation, histone deacetylation, histone methylation, and transcriptional regulation. Our data suggest that acetylation and methylation of chromatin associated with the ARHI promoter leads to loss of both ARHI expression and the ability to suppress tumor growth. Changes in chromatin that silence ARHI may be driven by methylation-dependent and -independent pathways. Reactivation of both the silenced paternal and imprinted maternal alleles can be achieved by demethylation and inhibition of histone deacetylation.
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Affiliation(s)
- Yinhua Yu
- Department of Experimental Therapeutics, The University of Texas, M. D. Anderson Cancer Center, Houston, Texas 77030, USA.
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Yoshida M, Kawachi K, Hamada Y, Nakata T, Kashu Y, Kikkawa H, Kadota M. [Surgical treatment for giant ascending aorta-arch aneurysm coexisted with DeBakey type II dissection on elderly women: report of a case]. Kyobu Geka 2003; 56:149-51. [PMID: 12635326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A 78-year-old woman was admitted to our hospital after computed tomography (CT) had revealed in her the presence of a giant ascending aorta-arch aneurysm. This aneurysm was about 8 cm in diameter and associated with DeBakey type II dissection. Aortography showed the same condition as the CT view with the entry on the ascending aorta. The ascending aortaarch was replaced with a Hemashield 24 mm, by using deep-hypothermic selective cerebral perfusion and the open distal method. There were no complications during her peripostoperative state and no evidence of leakage and remnant dissection on CT and aortography. This is a rare case in which thoracic aortic aneurysm coexisted with dissection. In this case of severe atherosclerosis, deep-hypothermic selective cerebral perfusion and the open distal method provided effective treatment.
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Affiliation(s)
- M Yoshida
- Department of Surgery II, Ehime University School of Medicine, Ehime, Japan
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Kadota M, Shirayoshi Y, Oshimura M. Elevated apoptosis in pre-mature neurons differentiated from mouse ES cells containing a single human chromosome 21. Biochem Biophys Res Commun 2002; 299:599-605. [PMID: 12459181 DOI: 10.1016/s0006-291x(02)02686-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A decrease in the number and density of neurons is the most common phenotype in the brains of Down syndrome (DS) patients, causing mental retardation. Studies using primary cultured neurons from DS patients or from model mice have suggested that a defect in metabolism of reactive oxygen species, or diminished levels of glutathione, causes mitochondrial and caspase-mediated neuronal apoptosis in vitro. However, it is not well documented whether neuronal apoptosis also occurs in immature DS neurons, owing to the difficulty in isolating or identifying neuronal stem cells in human or mouse fetuses. Here we utilized an in vitro model system for neuronal differentiation, with mouse embryonic stem cells containing human chromosome 21 (TT2F/hChr.21) to examine the effect of an additional hChr.21 on the early phases of neurogenesis. The differentiation profile of TT2F/hChr.21 cells was essentially the same as those of parental TT2F ES cells. In differentiations of both TT2F and TT2F/hChr.21 cells, high level of apoptosis was observed in neuronal stem cells, but the rate of apoptosis in TT2F/hChr.21 cells was significantly higher than that of parental cells. These results suggest that quantitative changes in the level of apoptosis in DS neuronal stem cells may account for the reduction of neuronal number and density in the DS brain.
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Affiliation(s)
- Mitsutaka Kadota
- Division of Molecular and Cell Genetics, Department of Molecular and Cellular Biology, Faculty of Medicine, School of Life Sciences, Tottori University, Nishimachi 86, Yonago, Tottori 683-8503, Japan
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Tsunooka N, Hamada Y, Nakata T, Takano S, Nakamura Y, Shikata A, Kawachi K, Kadota M. [A case of emergency coronary artery bypass graft for the patient using chronic hemodialysis, where in blood volume was measurable in the perioperative period]. Kyobu Geka 2002; 55:218-20. [PMID: 11889810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
An emergency coronary artery bypass graft (CABG) was given to a 66 year-old patient due to acute myocardial infarction (AMI). Circulating blood volume (BV) was measured to study in the perioperative period. Three coronary artery bypasses were made under cardiopulmonary bypass, being managed by ultrafiltration when the pump-oxygenator was in action and by peritoneal dialysis in the early postoperative period. Preoperative BV reduced immediately after the operation. It showed an increasing trend 4 hours after the operation, but after that BV reduced from that before the operation while water balance was kept positive. Cardiac output after the operation was higher than before. It suggested that in this patient using hemodialysis BV levels turned to be lower compared with that before the operation, as excessive water leaked out of the blood vessel, although water balance was kept positive due to improved cardiac functions after the operation.
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Affiliation(s)
- N Tsunooka
- Department of Surgery II, Ehime University School of Medicine, Ehime, Japan
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Arakawa A, Yamashita Y, Nakayama Y, Kadota M, Korogi H, Kawano O, Matsumoto M, Takahashi M. Assessment of lung volumes in pulmonary emphysema using multidetector helical CT: comparison with pulmonary function tests. Comput Med Imaging Graph 2001; 25:399-404. [PMID: 11390194 DOI: 10.1016/s0895-6111(01)00004-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The purpose of this study is to evaluate the usefulness of multidetector helical CT (MDCT) with three-dimensional (3D) postprocessing for assessing the lung volume at inspiration and expiration of the pulmonary emphysema and for comparing it with pulmonary function tests. Percentage lung volume at the threshold of -930, -900, -810, -790, and -770 at expiration showed good correlation with FEV1, FEV1/FVC, and DLCO/Va. Excellent correlation was observed between percentage lung volume at the threshold of -900 and FEV1/FVC. CT densitometry at expiration showed better correlation than that at inspiration with pulmonary function tests. MDCT with 3D technique is useful for assessing the severity of pulmonary emphysema.
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Affiliation(s)
- A Arakawa
- Department of Radiology, Kumamoto University Hospital, Kumamoto, Japan.
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Hamada Y, Kohtani T, Nakata T, Takano S, Tsunooka N, Kawachi K, Kadota M. [Blood transfusion under cardiopulmonary bypass is a possible inducer for inflammation?]. Kyobu Geka 2001; 54:835-8. [PMID: 11554072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
To investigate that blood transfusion under cardiopulmonary bypass is a possible inducer for inflammation, a retrospective study was made with 20 adult patients who underwent coronary artery bypass grafting. The subjects were divided into two groups; transfusion group (group T) including 9 patients who received blood transfusion during cardiopulmonary bypass and the control group (group C) including 11 patients who did not undergo perioperative transfusion. Respiratory index as an indicator of respiratory functions was determined before and immediately after cardiopulmonary bypass, at the end of surgery and 4 hours thereafter. Cardiac index and arterial pressure were determined as the indicator of cardiac function. Moreover, interleukin 6 and 8 (IL-6 and IL-8), inflammatory cytokines were measured and compared between the two groups. The mean amount of blood transfusion was 2.1 units per individual of group T. The minimum value of hematocrit during cardiopulmonary bypass was significantly lower in group T (15.8 +/- 1.8%) than group C (19.1 +/- 1.4%), but the difference became not significant after cardiopulmonary bypass. There were no significant differences either in aortic pressure or cardiac index between two groups. The respiratory index at the end of surgery was higher in group T but the difference was not significant. Meanwhile IL-8 level at the end of cardiopulmonary bypass was significantly higher in group T (67.9 +/- 36 pg/ml) than group C (35.1 +/- 21 pg/ml). However, there was no difference in IL-6 level between the two. These results suggested that inflammation might be aggravated by an increase of IL-8 induced by blood transfusion.
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Affiliation(s)
- Y Hamada
- Department of Surgery II, Ehime University School of Medicine, Ehime, Japan
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50
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Nakayama Y, Yamashita Y, Kadota M, Takahashi M, Kanemitsu K, Hiraoka T, Hirota M, Ogawa M, Takeya M. Vascular encasement by pancreatic cancer: correlation of CT findings with surgical and pathologic results. J Comput Assist Tomogr 2001; 25:337-42. [PMID: 11351180 DOI: 10.1097/00004728-200105000-00002] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE The purpose of this study was to correlate thin-slice high-resolution helical CT findings of arterial and venous involvement in pancreatic cancers with surgical and histopathologic results. METHOD Forty-eight patients with pancreatic cancer underwent preoperative thin-slice high-resolution helical CT, followed by surgical dissection of the pancreatic vessels during curative or palliative surgery. Major vessels running within 1 cm from the tumor margin were evaluated. CT appearance was graded on a 0-4 scale (0: none, 1: <24%, 2: 25-49%, 3: 50-74%, 4: 75-100%) by circumferential contiguity of tumor to vessels. Resected specimens were available from 26 patients. RESULTS Surgical correlation of CT findings was available in 89 veins and 83 arteries, and both surgical and histologic correlation was available for 42 veins and 29 arteries. At surgical observation, 29 of 35 veins (82.9%) evaluated as CT grade 3 or 4 were found to be involved, whereas only 18 of 30 arteries (60%) evaluated as CT grade 3 or 4 were proved to be involved. On microscopic observation, tumor invasion to the portal venous systems was confirmed in 15 of 42 (35.7%) vessels, and this invasion was depicted as from CT grades 1 to 4. In arteries, tumor invasion was seen in 3 of 29 vessels (10.3%), all of which were graded as 3 or 4 by CT. CONCLUSION The grading system of vascular invasion should differ between arteries and veins. Involvement of the venous system exceeding one-half circumference of the vessels (grade 3 or 4) was suggestive of vascular invasion; however, this criterion was not always satisfactory for the evaluation of tumor invasion in the arterial system.
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Affiliation(s)
- Y Nakayama
- Department of Radiology, Kumamoto University School of Medicine, Japan.
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