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Kong Y, Börner K. Publication, funding, and experimental data in support of Human Reference Atlas construction and usage. Sci Data 2024; 11:574. [PMID: 38834597 PMCID: PMC11150433 DOI: 10.1038/s41597-024-03416-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage.
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Affiliation(s)
- Yongxin Kong
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
- School of Information Management, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Katy Börner
- Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
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2
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Kamata M, Taniguchi Y, Yaguchi J, Tanaka H, Yaguchi S. Nonmuscular Troponin-I is required for gastrulation in sea urchin embryos. Dev Dyn 2024; 253:624-628. [PMID: 38071599 DOI: 10.1002/dvdy.680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Gastrulation is one of the most important events in our lives (Barresi and Gilbert, 2020, Developmental Biology, 12th ed.). The molecular mechanisms of gastrulation in multicellular organisms are not yet fully understood, since many molecular, physical, and chemical factors are involved in the event. RESULTS Here, we found that one of muscle components, Troponin-I (TnI), is expressed in future gut cells, which are not muscular cells at all, and regulates gastrulation in embryos of a sea urchin, Hemicentrotus pulcherrimus. When we block the function of TnI, the invagination was inhibited in spite that the gut-cell specifier gene is normally expressed. In addition, blocking myosin activity also induced incomplete gastrulation. CONCLUSION These results strongly suggested that TnI regulates nonmuscular actin-myosin interactions during sea urchin gastrulation. So far, Troponin system is treated as specific only for muscle components, especially for striated muscle, but our data clearly show that TnI is involved in nonmuscular event. It is also reported that recent sensitive gene expression analysis revealed that Troponin genes are expressed in nonmuscular tissues in mammals (Ono et al., Sci Data, 2017;4:170105). These evidences propose the new evolutionary and functional scenario of the involvement of Troponin system in nonmuscular cell behaviors using actin-myosin system in bilaterians including human being.
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Affiliation(s)
- Mai Kamata
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Yuri Taniguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Junko Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Hiroyuki Tanaka
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
| | - Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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Yamada N, Karasawa T, Ito J, Yamamuro D, Morimoto K, Nakamura T, Komada T, Baatarjav C, Saimoto Y, Jinnouchi Y, Watanabe K, Miura K, Yahagi N, Nakagawa K, Matsumura T, Yamada KI, Ishibashi S, Sata N, Conrad M, Takahashi M. Inhibition of 7-dehydrocholesterol reductase prevents hepatic ferroptosis under an active state of sterol synthesis. Nat Commun 2024; 15:2195. [PMID: 38472233 DOI: 10.1038/s41467-024-46386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Recent evidence indicates ferroptosis is implicated in the pathophysiology of various liver diseases; however, the organ-specific regulation mechanism is poorly understood. Here, we demonstrate 7-dehydrocholesterol reductase (DHCR7), the terminal enzyme of cholesterol biosynthesis, as a regulator of ferroptosis in hepatocytes. Genetic and pharmacological inhibition (with AY9944) of DHCR7 suppress ferroptosis in human hepatocellular carcinoma Huh-7 cells. DHCR7 inhibition increases its substrate, 7-dehydrocholesterol (7-DHC). Furthermore, exogenous 7-DHC supplementation using hydroxypropyl β-cyclodextrin suppresses ferroptosis. A 7-DHC-derived oxysterol metabolite, 3β,5α-dihydroxycholest-7-en-6-one (DHCEO), is increased by the ferroptosis-inducer RSL-3 in DHCR7-deficient cells, suggesting that the ferroptosis-suppressive effect of DHCR7 inhibition is associated with the oxidation of 7-DHC. Electron spin resonance analysis reveals that 7-DHC functions as a radical trapping agent, thus protecting cells from ferroptosis. We further show that AY9944 inhibits hepatic ischemia-reperfusion injury, and genetic ablation of Dhcr7 prevents acetaminophen-induced acute liver failure in mice. These findings provide new insights into the regulatory mechanism of liver ferroptosis and suggest a potential therapeutic option for ferroptosis-related liver diseases.
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Affiliation(s)
- Naoya Yamada
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, Shimotsuke, Tochigi, Japan.
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Bavaria, Germany.
| | - Tadayoshi Karasawa
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.
| | - Junya Ito
- Laboratory of Food Function Analysis, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Daisuke Yamamuro
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Kazushi Morimoto
- Department of Molecular Pathobiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Toshitaka Nakamura
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Bavaria, Germany
| | - Takanori Komada
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Chintogtokh Baatarjav
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Yuma Saimoto
- Department of Molecular Pathobiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yuka Jinnouchi
- Department of Molecular Pathobiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Kazuhisa Watanabe
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Kouichi Miura
- Division of Gastroenterology, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Naoya Yahagi
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Kiyotaka Nakagawa
- Laboratory of Food Function Analysis, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Takayoshi Matsumura
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Ken-Ichi Yamada
- Department of Molecular Pathobiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Shun Ishibashi
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Naohiro Sata
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Marcus Conrad
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Bavaria, Germany
| | - Masafumi Takahashi
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan.
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Kamihara T, Kinoshita T, Kawano R, Tanaka S, Toda A, Ohara F, Hirashiki A, Kokubo M, Shimizu A. Upregulated Genes in Atrial Fibrillation Blood and the Left Atrium. Cardiology 2024; 149:357-368. [PMID: 38452746 DOI: 10.1159/000537923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
INTRODUCTION Atrial fibrillation (AF) is a common arrhythmia associated with aging. Many known risk factors are associated with AF, but many senior individuals do not develop AF despite having multiple risk factors. This finding suggests that other factors may be involved in AF onset. This study aimed to identify upregulated genes in the peripheral blood and left atrium of patients with AF. These genes may serve as potential biomarkers to predict AF onset risk and its complications. METHODS Gene expression data were analyzed from blood (n = 3) and left atrial samples (n = 15) of patients with AF and sinus rhythm. We evaluated the significant genes identified using p value analysis of weighted average difference to confirm their rankings. We created figures for the genes using GeneMANIA and performed a functional analysis using Cytoscape3.10.1. Hub and bottleneck genes were identified based on degree and betweenness centrality. We used reference expression (RefEx) to confirm the organs in which the extracted genes were expressed. Heatmaps and Gene ontology term evaluation were performed to further elucidate the biological functions of the genes. RESULTS We identified 12 upregulated genes (CAST, ASAH1, MAFB, VCAN, DDIT4, FTL, HEXB, PROS1, BNIP3L, PABPC1, YBX3, and S100A6) in both the blood and left atrium of patients with AF. We analyzed the gene functions using GeneMANIA and Cytoscape. The identified genes were involved in a variety of pathways, including lysosomal function and lipid and sphingolipid catabolism. Next, we investigated whether the 12 identified genes identified were systemically expressed or had high organ specificity. Finally, RefEx was used to analyze the gene expression levels in various tissues. Four genes, FTL, ASAH1, S100A6, and PABPC1, were highly expressed in the normal heart tissue. Finally, we evaluated the expression levels of the 12 genes in the blood of patients with AF using a heatmap. Our findings suggest that the 12 genes identified in this study, especially the lysosome-related genes (FTL and ASAH1), may be involved in AF pathogenesis. CONCLUSION Lysosome-related genes may be important to understand the AF pathophysiology and to develop AF-related future studies.
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Affiliation(s)
- Takahiro Kamihara
- Department of Cardiology, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Tomoyasu Kinoshita
- Innovation Center for Translational Research, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Reo Kawano
- Innovation Center for Translational Research, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Seiya Tanaka
- Innovation Center for Translational Research, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Ayano Toda
- Innovation Center for Translational Research, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Fumiya Ohara
- Department of Hematology, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Akihiro Hirashiki
- Department of Cardiology, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Manabu Kokubo
- Department of Cardiology, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Atsuya Shimizu
- Department of Cardiology, National Center for Geriatrics and Gerontology, Obu, Japan
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Tsuyuzaki K, Ishii M, Nikaido I. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC Bioinformatics 2023; 24:420. [PMID: 37936079 PMCID: PMC10631077 DOI: 10.1186/s12859-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/21/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs. RESULTS In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. CONCLUSIONS Through extensive studies with simulated and empirical datasets, we have shown that scTensor can detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships. scTensor is implemented as a freely available R/Bioconductor package.
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Affiliation(s)
- Koki Tsuyuzaki
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Japan Science and Technology Agency, PRESTO, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Manabu Ishii
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Department of Functional Genome Informatics, Division of Biological Data Science, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Miyoshi H, Otomo M, Takahashi K. Clomipramine inhibits dynamin GTPase activity by L-α-phosphatidyl-L-serine stimulation. J Biochem 2023; 174:267-272. [PMID: 37137298 DOI: 10.1093/jb/mvad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Three dynamin isoforms play critical roles in clathrin-dependent endocytosis. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells via clathrin-dependent endocytosis. We previously reported that 3-(3-chloro-10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine (clomipramine) inhibits the GTPase activity of dynamin 1, which is in mainly neuron. Therefore, we investigated whether clomipramine inhibits the activity of other dynamin isoforms in this study. We found that, similar to its inhibitory effect on dynamin 1, clomipramine inhibited the l-α-phosphatidyl-l-serine-stimulated GTPase activity of dynamin 2, which is expressed ubiquitously, and dynamin 3, which is expressed in the lung. Inhibition of GTPase activity raises the possibility that clomipramine can suppress SARS-CoV-2 entry into host cells.
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Affiliation(s)
- Hiroshi Miyoshi
- Department of Microbiology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki 216-8511, Japan
| | - Masahiro Otomo
- Department of Neuropsychiatry, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki 216-8511, Japan
| | - Kiyofumi Takahashi
- Department of Neuropsychiatry, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae, Kawasaki 216-8511, Japan
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7
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Watanabe Y, Takeda H, Honda N, Hanajima R. A bioinformatic investigation of proteasome and autophagy expression in the central nervous system. Heliyon 2023; 9:e18188. [PMID: 37519643 PMCID: PMC10375789 DOI: 10.1016/j.heliyon.2023.e18188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
The ubiquitin proteasome system (UPS) and autophagy lysosome pathway (ALP) are crucial in the control of protein quality. However, data regarding the relative significance of UPS and ALP in the central nervous system (CNS) are limited. In the present study, using publicly available data, we computed the quantitative expression status of UPS- and ALP-related genes and their products in the CNS as compared with that in other tissues and cells. We obtained human and mouse gene expression datasets from the reference expression dataset (RefEx) and Genevestigator (a tool for handling curated transcriptomic data from public repositories) as well as human proteomics data from the proteomics database (ProteomicsDB). The expression levels of genes and proteins in four categories-ubiquitin, proteasome, autophagy, and lysosome--in the cells and tissues were assessed. Perturbation of the gene expression by drugs was also analyzed for the four categories. Compared with that for ubiquitin, autophagy, and lysosome, gene expression for proteasome was consistently lower in the CNS of mice but was more pronounced in humans. Neural stem cells and neurons showed low proteasome gene expression as compared with embryonic stem cells. Proteomic analyses, however, did not show trends similar to those observed in the gene expression analyses. Perturbation analyses revealed that azithromycin and vitamin D3 upregulated the expression of both UPS and ALP. Gene and proteomic expression data could offer a fresh perspective on CNS pathophysiology. Our results indicate that disproportional expression of UPS and ALP might affect CNS disorders and that this imbalance might be redressed by several therapeutic candidates.
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Affiliation(s)
- Yasuhiro Watanabe
- Corresponding author. Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, 36-1, Nishi-cho, Yonago, Japan.
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2022; 40:1774-1779. [PMID: 35798960 PMCID: PMC10277029 DOI: 10.1038/s41587-022-01368-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/20/2022] [Indexed: 01/30/2023]
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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9
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Ozawa M, Hattori Y, Higo S, Otsuka M, Matsumoto K, Ozawa H, Ishii H. Optimized Mouse-on-mouse Immunohistochemical Detection of Mouse ESR2 Proteins with PPZ0506 Monoclonal Antibody. Acta Histochem Cytochem 2022; 55:159-168. [PMID: 36405553 PMCID: PMC9631985 DOI: 10.1267/ahc.22-00043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/05/2022] [Indexed: 12/01/2023] Open
Abstract
Despite the physiological significance of ESR2, a lack of well-validated detection systems for ESR2 proteins has hindered progress in ESR2 research. Thus, recent identification of a specific anti-human ESR2 monoclonal antibody (PPZ0506) and its specific cross-reactivity against mouse and rat ESR2 proteins heightened momenta toward development of appropriate immunohistochemical detection systems for rodent ESR2 proteins. Building upon our previous optimization of ESR2 immunohistochemical detection in rats using PPZ0506, in this study, we further aimed to optimize mouse-on-mouse immunohistochemical detection using PPZ0506. Our assessment of several staining conditions using paraffin-embedded ovary sections revealed that intense heat-induced antigen retrieval, appropriate blocking, and appropriate antibody dilutions were necessary for optimization of mouse-on-mouse immunohistochemistry. Subsequently, we applied the optimized immunostaining method to determine expression profiles of mouse ESR2 proteins in peripheral tissues and brain subregions. Our analyses revealed more localized distribution of mouse ESR2 proteins than previously assumed. Moreover, comparison of these results with those obtained in humans and rats using PPZ0506 revealed interspecies differences in ESR2 expression. We expect that our optimized methodology for immunohistochemical staining of mouse ESR2 proteins will help researchers to solve multiple lines of controversial evidence concerning ESR2 expression.
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Affiliation(s)
- Mina Ozawa
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Yujiro Hattori
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Shimpei Higo
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Mai Otsuka
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Keisuke Matsumoto
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Hitoshi Ozawa
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
- School of Health Sciences, Bukkyo University, 7, Nishinokyo Higashitoganocho, Nakagyo-ku, Kyoto 604–8418, Japan
| | - Hirotaka Ishii
- Department of Anatomy and Neurobiology, Graduate School of Medicine, Nippon Medical School, 1–1–5, Sendagi, Bunkyo-ku, Tokyo 113–8602, Japan
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10
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Fukazawa T, Tanimoto K, Yamaoka E, Kojima M, Kanawa M, Hirohashi N, Hiyama E. Oncogenic Role of ADAM32 in Hepatoblastoma: A Potential Molecular Target for Therapy. Cancers (Basel) 2022; 14:cancers14194732. [PMID: 36230656 PMCID: PMC9562177 DOI: 10.3390/cancers14194732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 11/16/2022] Open
Abstract
Outcomes of pediatric hepatoblastoma (HBL) have improved, but refractory cases still occur. More effective and safer drugs are needed that are based on molecular mechanisms. A disintegrin and metalloproteases (ADAMs) are expressed with high frequency in various human carcinomas and play an important role in cancer progression. In this study, we analyzed expression of ADAMs in HBL with a cDNA microarray dataset and found that the expression level of ADAM32 is particularly high. To investigate the role of ADAM32 in cancer, forced expression or knockdown experiments were conducted with HepG2 and HBL primary cells. Colony formation, cell migration and invasion, and cell viability were increased in HepG2 expressing ADAM32, whereas knockdown of ADAM32 induced a decrease in these cellular functions. Quantitative RT-PCR demonstrated an association between ADAM32 expression and the expression of genes related to cancer stem cells and epithelial–mesenchymal transition (EMT), suggesting a role of ADAM32 in cancer stemness and EMT. Furthermore, knockdown of ADAM32 increased cisplatin-induced apoptosis, and this effect was attenuated by a caspase-8 inhibitor, suggesting that ADAM32 plays a role in extrinsic apoptosis signaling. We conclude that ADAM32 plays a crucial role in progression of HBL, so it might be a promising molecular target in anticancer therapy.
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Affiliation(s)
- Takahiro Fukazawa
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima 734-8553, Japan
| | - Keiji Tanimoto
- Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- Correspondence: (K.T.); (E.H.); Tel.: +81-(0)82-257-5841 (K.T.); +81-(0)82-257-5555 (E.H.)
| | - Emi Yamaoka
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima 734-8553, Japan
| | - Masato Kojima
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Masami Kanawa
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima 734-8553, Japan
| | - Nobuyuki Hirohashi
- Department of Radiation Disaster Medicine, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Eiso Hiyama
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima 734-8553, Japan
- Correspondence: (K.T.); (E.H.); Tel.: +81-(0)82-257-5841 (K.T.); +81-(0)82-257-5555 (E.H.)
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11
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New Drug Development and Clinical Trial Design by Applying Genomic Information Management. Pharmaceutics 2022; 14:pharmaceutics14081539. [PMID: 35893795 PMCID: PMC9330622 DOI: 10.3390/pharmaceutics14081539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Depending on the patients’ genotype, the same drug may have different efficacies or side effects. With the cost of genomic analysis decreasing and reliability of analysis methods improving, vast amount of genomic information has been made available. Several studies in pharmacology have been based on genomic information to select the optimal drug, determine the dose, predict efficacy, and prevent side effects. This paper reviews the tissue specificity and genomic information of cancer. If the tissue specificity of cancer is low, cancer is induced in various organs based on a single gene mutation. Basket trials can be performed for carcinomas with low tissue specificity, confirming the efficacy of one drug for a single gene mutation in various carcinomas. Conversely, if the tissue specificity of cancer is high, cancer is induced in only one organ based on a single gene mutation. An umbrella trial can be performed for carcinomas with a high tissue specificity. Some drugs are effective for patients with a specific genotype. A companion diagnostic strategy that prescribes a specific drug for patients selected with a specific genotype is also reviewed. Genomic information is used in pharmacometrics to identify the relationship among pharmacokinetics, pharmacodynamics, and biomarkers of disease treatment effects. Utilizing genomic information, sophisticated clinical trials can be designed that will be better suited to the patients of specific genotypes. Genomic information also provides prospects for innovative drug development. Through proper genomic information management, factors relating to drug response and effects can be determined by selecting the appropriate data for analysis and by understanding the structure of the data. Selecting pre-processing and appropriate machine-learning libraries for use as machine-learning input features is also necessary. Professional curation of the output result is also required. Personalized medicine can be realized using a genome-based customized clinical trial design.
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12
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Smooth muscle protein 22α-Cre recombination in resting cardiac fibroblasts and hematopoietic precursors. Sci Rep 2022; 12:11564. [PMID: 35798848 PMCID: PMC9263136 DOI: 10.1038/s41598-022-15957-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
The Cre-loxP system has been widely used for cell- or organ-specific gene manipulation, but it is important to precisely understand what kind of cells the recombination takes place in. Smooth muscle 22α (SM22α)-Cre mice have been utilized to alter genes in vascular smooth muscle cells (VSMCs), activated fibroblasts or cardiomyocytes (CMs). Moreover, previous reports indicated that SM22α-Cre is expressed in adipocytes, platelets or myeloid cells. However, there have been no report of whether SM22α-Cre recombination takes place in nonCMs in hearts. Thus, we used the double-fluorescent Cre reporter mouse in which GFP is expressed when recombination occurs. Immunofluorescence analysis demonstrated that recombination occurred in resting cardiac fibroblasts (CFs) or macrophages, as well as VSMCs and CMs. Flow cytometry showed that some CFs, resident macrophages, neutrophils, T cells, and B cells were positive for GFP. These results prompted us to analyze bone marrow cells, and we observed GFP-positive hematopoietic precursor cells (HPCs). Taken together, these results indicated that SM22α-Cre-mediated recombination occurs in resting CFs and hematopoietic cell lineages, including HPCs, which is a cautionary point when using SM22α-Cre mice.
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13
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Clarke T, Fernandez FE, Dawson PA. Sulfation Pathways During Neurodevelopment. Front Mol Biosci 2022; 9:866196. [PMID: 35495624 PMCID: PMC9047184 DOI: 10.3389/fmolb.2022.866196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Sulfate is an important nutrient that modulates a diverse range of molecular and cellular functions in mammalian physiology. Over the past 2 decades, animal studies have linked numerous sulfate maintenance genes with neurological phenotypes, including seizures, impaired neurodevelopment, and behavioral abnormalities. Despite sulfation pathways being highly conserved between humans and animals, less than one third of all known sulfate maintenance genes are clinically reportable. In this review, we curated the temporal and spatial expression of 91 sulfate maintenance genes in human fetal brain from 4 to 17 weeks post conception using the online Human Developmental Biology Resource Expression. In addition, we performed a systematic search of PubMed and Embase, identifying those sulfate maintenance genes linked to atypical neurological phenotypes in humans and animals. Those findings, together with a search of the Online Mendelian Inheritance in Man database, identified a total of 18 candidate neurological dysfunction genes that are not yet considered in clinical settings. Collectively, this article provides an overview of sulfate biology genes to inform future investigations of perturbed sulfate homeostasis associated with neurological conditions.
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Affiliation(s)
- Taylor Clarke
- School of Behavioural and Health Sciences, Faculty of Health Sciences, Australian Catholic University, Banyo, QLD, Australia
| | - Francesca E. Fernandez
- School of Behavioural and Health Sciences, Faculty of Health Sciences, Australian Catholic University, Banyo, QLD, Australia
| | - Paul A. Dawson
- Mater Research Institute, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Paul A. Dawson,
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14
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Loss of KAP3 decreases intercellular adhesion and impairs intracellular transport of laminin in signet ring cell carcinoma of the stomach. Sci Rep 2022; 12:5050. [PMID: 35322078 PMCID: PMC8943207 DOI: 10.1038/s41598-022-08904-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Signet-ring cell carcinoma (SRCC) is a unique subtype of gastric cancer that is impaired for cell-cell adhesion. The pathogenesis of SRCC remains unclear. Here, we show that expression of kinesin-associated protein 3 (KAP3), a cargo adaptor subunit of the kinesin superfamily protein 3 (KIF3), a motor protein, is specifically decreased in SRCC of the stomach. CRISPR/Cas9-mediated gene knockout experiments indicated that loss of KAP3 impairs the formation of circumferential actomyosin cables by inactivating RhoA, leading to the weakening of cell-cell adhesion. Furthermore, in KAP3 knockout cells, post-Golgi transport of laminin, a key component of the basement membrane, was inhibited, resulting in impaired basement membrane formation. Together, these findings uncover a potential role for KAP3 in the pathogenesis of SRCC of the stomach.
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15
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Fukushima A, Takahashi M, Nagasaki H, Aono Y, Kobayashi M, Kusano M, Saito K, Kobayashi N, Arita M. Development of RIKEN Plant Metabolome MetaDatabase. PLANT & CELL PHYSIOLOGY 2022; 63:433-440. [PMID: 34918130 PMCID: PMC8917833 DOI: 10.1093/pcp/pcab173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The advancement of metabolomics in terms of techniques for measuring small molecules has enabled the rapid detection and quantification of numerous cellular metabolites. Metabolomic data provide new opportunities to gain a deeper understanding of plant metabolism that can improve the health of both plants and humans that consume them. Although major public repositories for general metabolomic data have been established, the community still has shortcomings related to data sharing, especially in terms of data reanalysis, reusability and reproducibility. To address these issues, we developed the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM, http://metabobank.riken.jp/pmm/db/plantMetabolomics), which stores mass spectrometry-based (e.g. gas chromatography-MS-based) metabolite profiling data of plants together with their detailed, structured experimental metadata, including sampling and experimental procedures. Our metadata are described as Linked Open Data based on the Resource Description Framework using standardized and controlled vocabularies, such as the Metabolomics Standards Initiative Ontology, which are to be integrated with various life and biomedical science data using the World Wide Web. RIKEN PMM implements intuitive and interactive operations for plant metabolome data, including raw data (netCDF format), mass spectra (NIST MSP format) and metabolite annotations. The feature is suitable not only for biologists who are interested in metabolomic phenotypes, but also for researchers who would like to investigate life science in general through plant metabolomic approaches.
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Affiliation(s)
| | - Mikiko Takahashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | | | - Yusuke Aono
- Degree Programs in Life and Earth Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Makoto Kobayashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyako Kusano
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Faculty of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuki Saito
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Norio Kobayashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Data Knowledge Organization Unit, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masanori Arita
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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16
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Takatsuka H, Fahmi M, Hamanishi K, Sakuratani T, Kubota Y, Ito M. In silico Analysis of SARS-CoV-2 ORF8-Binding Proteins Reveals the Involvement of ORF8 in Acquired-Immune and Innate-Immune Systems. Front Med (Lausanne) 2022; 9:824622. [PMID: 35178414 PMCID: PMC8844466 DOI: 10.3389/fmed.2022.824622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of a new type of coronavirus infection, COVID-19, which has rapidly spread worldwide. The overall genome sequence homology between SARS-CoV-2 and SARS-CoV is 79%. However, the homology of the ORF8 protein between these two coronaviruses is low, at ~26%. Previously, it has been suggested that infection by the ORF8-deleted variant of SARS-CoV-2 results in less severe symptoms than in the case of wild-type SARS-CoV-2. Although we found that ORF8 is involved in the proteasome autoimmunity system, the precise role of ORF8 in infection and pathology has not been fully clarified. In this study, we determined a new network of ORF8-interacting proteins by performing in silico analysis of the binding proteins against the previously described 47 ORF8-binding proteins. We used as a dataset 431 human protein candidates from Uniprot that physically interacted with 47 ORF8-binding proteins, as identified using STRING. Homology and phylogenetic profile analyses of the protein dataset were performed on 446 eukaryotic species whose genome sequences were available in KEGG OC. Based on the phylogenetic profile results, clustering analysis was performed using Ward's method. Our phylogenetic profiling showed that the interactors of the ORF8-interacting proteins were clustered into three classes that were conserved across chordates (Class 1: 152 proteins), metazoans (Class 2: 163 proteins), and eukaryotes (Class 3: 114 proteins). Following the KEGG pathway analysis, classification of cellular localization, tissue-specific expression analysis, and a literature study on each class of the phylogenetic profiling cluster tree, we predicted that the following: protein members in Class 1 could contribute to COVID-19 pathogenesis via complement and coagulation cascades and could promote sarcoidosis; the members of Class 1 and 2, together, may contribute to the downregulation of Interferon-β; and Class 3 proteins are associated with endoplasmic reticulum stress and the degradation of human leukocyte antigen.
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Affiliation(s)
- Hisashi Takatsuka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Muhamad Fahmi
- Research Department, Research Institute for Humanity and Nature, Kyoto, Japan.,Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Japan
| | - Kotono Hamanishi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Takuya Sakuratani
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
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17
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Lestari B, Naito S, Endo A, Nishihara H, Kato A, Watanabe E, Denda K, Komada M, Fukushima T. Placental mammals acquired functional sequences in NRK for regulating the CK2-PTEN-AKT pathway and placental cell proliferation. Mol Biol Evol 2022; 39:6499274. [PMID: 34999820 PMCID: PMC8857918 DOI: 10.1093/molbev/msab371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The molecular evolution processes underlying the acquisition of the placenta in eutherian ancestors are not fully understood. Mouse NCK-interacting kinase (NIK)-related kinase (NRK) is expressed highly in the placenta and plays a role in preventing placental hyperplasia. Here, we show the molecular evolution of NRK, which confers its function for inhibiting placental cell proliferation. Comparative genome analysis identified NRK orthologs across vertebrates, which share the kinase and citron homology (CNH) domains. Evolutionary analysis revealed that NRK underwent extensive amino acid substitutions in the ancestor of placental mammals and has been since conserved. Biochemical analysis of mouse NRK revealed that the CNH domain binds to phospholipids, and a region in NRK binds to and inhibits casein kinase-2 (CK2), which we named the CK2-inhibitory region (CIR). Cell culture experiments suggest the following: 1) Mouse NRK is localized at the plasma membrane via the CNH domain, where the CIR inhibits CK2. 2) This mitigates CK2-dependent phosphorylation and inhibition of PTEN and 3) leads to the inhibition of AKT signaling and cell proliferation. Nrk deficiency increased phosphorylation levels of PTEN and AKT in mouse placenta, supporting our hypothesis. Unlike mouse NRK, chicken NRK did not bind to phospholipids and CK2, decrease phosphorylation of AKT, or inhibit cell proliferation. Both the CNH domain and CIR have evolved under purifying selection in placental mammals. Taken together, our study suggests that placental mammals acquired the phospholipid-binding CNH domain and CIR in NRK for regulating the CK2–PTEN–AKT pathway and placental cell proliferation.
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Affiliation(s)
- Beni Lestari
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Satomi Naito
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Akinori Endo
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Erika Watanabe
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Kimitoshi Denda
- School of Life Science and Technology, Tokyo Institute of Technology, Japan
| | - Masayuki Komada
- School of Life Science and Technology, Tokyo Institute of Technology, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Toshiaki Fukushima
- School of Life Science and Technology, Tokyo Institute of Technology, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
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18
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Yokosaki Y, Nishimichi N. New Therapeutic Targets for Hepatic Fibrosis in the Integrin Family, α8β1 and α11β1, Induced Specifically on Activated Stellate Cells. Int J Mol Sci 2021; 22:ijms222312794. [PMID: 34884600 PMCID: PMC8657911 DOI: 10.3390/ijms222312794] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022] Open
Abstract
A huge effort has been devoted to developing drugs targeting integrins over 30 years, because of the primary roles of integrins in the cell-matrix milieu. Five αv-containing integrins, in the 24 family members, have been a central target of fibrosis. Currently, a small molecule against αvβ1 is undergoing a clinical trial for NASH-associated fibrosis as a rare agent aiming at fibrogenesis. Latent TGFβ activation, a distinct talent of αv-integrins, has been intriguing as a therapeutic target. None of the αv-integrin inhibitors, however, has been in the clinical market. αv-integrins commonly recognize an Arg-Gly-Asp (RGD) sequence, and thus the pharmacophore of inhibitors for the 5-integrins is based on the same RGD structure. The RGD preference of the integrins, at the same time, dilutes ligand specificity, as the 5-integrins share ligands containing RGD sequence such as fibronectin. With the inherent little specificity in both drugs and targets, "disease specificity" has become less important for the inhibitors than blocking as many αv-integrins. In fact, an almighty inhibitor for αv-integrins, pan-αv, was in a clinical trial. On the contrary, approved integrin inhibitors are all specific to target integrins, which are expressed in a cell-type specific manner: αIIbβ3 on platelets, α4β1, α4β7 and αLβ2 on leukocytes. Herein, "disease specific" integrins would serve as attractive targets. α8β1 and α11β1 are selectively expressed in hepatic stellate cells (HSCs) and distinctively induced upon culture activation. The exceptional specificity to activated HSCs reflects a rather "pathology specific" nature of these new integrins. The monoclonal antibodies against α8β1 and α11β1 in preclinical examinations may illuminate the road to the first medical agents.
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19
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Endo Y, Asanuma D, Namiki S, Sugihara K, Hirose K, Uemura A, Kubota Y, Miura T. Quantitative modeling of regular retinal microglia distribution. Sci Rep 2021; 11:22671. [PMID: 34811401 PMCID: PMC8608893 DOI: 10.1038/s41598-021-01820-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Microglia are resident immune cells in the central nervous system, showing a regular distribution. Advancing microscopy and image processing techniques have contributed to elucidating microglia’s morphology, dynamics, and distribution. However, the mechanism underlying the regular distribution of microglia remains to be elucidated. First, we quantitatively confirmed the regularity of the distribution pattern of microglial soma in the retina. Second, we formulated a mathematical model that includes factors that may influence regular distribution. Next, we experimentally quantified the model parameters (cell movement, process formation, and ATP dynamics). The resulting model simulation from the measured parameters showed that direct cell–cell contact is most important in generating regular cell spacing. Finally, we tried to specify the molecular pathway responsible for the repulsion between neighboring microglia.
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Affiliation(s)
- Yoshie Endo
- Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Asanuma
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeyuki Namiki
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kei Sugihara
- Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenzo Hirose
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Aichi, Japan
| | - Yoshiaki Kubota
- Department of Anatomy, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Miura
- Department of Anatomy and Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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20
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Mohammadi M, Salehzadeh A, Talesh Sasani S, Tarang A. rs6426881 in the 3'-UTR of PBX1 is involved in breast and gastric cancers via altering the binding potential of miR-522-3p. Mol Biol Rep 2021; 48:7405-7414. [PMID: 34655407 DOI: 10.1007/s11033-021-06756-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Breast and gastric cancers are the most important diseases that lead to cancer death and social healthcare challenge. Overexpression of PBX1, a proto-oncogene, is correlated with the progression and metastasis of various cancers. For the first time, in this study the researchers evaluated the relationship between rs6426881, affecting miR-522-3p binding to the PBX1, with breast and gastric cancers. METHODS AND RESULTS The Microarray analysis was performed for finding the relative expression level of PBX1 and hsa-miR-522-3p, based on high throughput experiments. The GSE54397, GSE112369, GSE10810, GSE241585.ER, GSE24185.PR, GSE68373, and GSE38167 datasets were analyzed. A case-control study was carried out in 123 Iranian suffering from breast cancer and 132 participants as control samples as well as 130 people suffering from gastric cancer and 54 people as control group members. SNP rs6426881 in the 3'-UTR of PBX1 was genotyped by the High-Resolution Melting (HRM) method. Association analysis revealed that rs6426881 is correlated with Estrogen and Progesterone receptors, grade, and stage of breast cancer. Furthermore, a significant relationship was observed between the genotypes and blood groups in gastric cancer, while the distribution of alleles was significantly related to smoking, status of the primary tumor, and metastasis (Chi-Square P < 0.05). Finally, Bioinformatics analyses suggested that rs6426881 contains binding sites for miR-522-3p in the 3'-UTR of PBX1 transcript. The finding suggested that TT genotype is associated with poor prognosis in breast and gastric cancer. CONCLUSIONS The rs6426881 T allele at PBX1 3'-UT is significantly related to breast and gastric cancers by altering the regulatory affinity of miR-522-3p to PBX1 3'-UTR and may be suggested as a novel prognostic biomarker for the diseases.
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Affiliation(s)
- Maryam Mohammadi
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran.
| | | | - Alireza Tarang
- Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran
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21
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Kasprzycka W, Trębińska-Stryjewska A, Lewandowski RB, Stępińska M, Osuchowska PN, Dobrzyńska M, Achour Y, Osuchowski ŁP, Starzyński J, Mierczyk Z, Trafny EA. Nanosecond Pulsed Electric Field Only Transiently Affects the Cellular and Molecular Processes of Leydig Cells. Int J Mol Sci 2021; 22:ijms222011236. [PMID: 34681896 PMCID: PMC8541366 DOI: 10.3390/ijms222011236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/11/2022] Open
Abstract
The purpose of this study was to verify whether the nanosecond pulsed electric field, not eliciting thermal effects, permanently changes the molecular processes and gene expression of Leydig TM3 cells. The cells were exposed to a moderate electric field (80 quasi-rectangular shape pulses, 60 ns pulse width, and an electric field of 14 kV/cm). The putative disturbances were recorded over 24 h. After exposure to the nanosecond pulsed electric field, a 19% increase in cell diameter, a loss of microvilli, and a 70% reduction in cell adhesion were observed. Some cells showed the nonapoptotic externalization of phosphatidylserine through the pores in the plasma membrane. The cell proportion in the subG1 phase increased by 8% at the expense of the S and G2/M phases, and the DNA was fragmented in a small proportion of the cells. The membrane mitochondrial potential and superoxide content decreased by 37% and 23%, respectively. Microarray’s transcriptome analysis demonstrated a negative transient effect on the expression of genes involved in oxidative phosphorylation, DNA repair, cell proliferation, and the overexpression of plasma membrane proteins. We conclude that nanosecond pulsed electric field affected the physiology and gene expression of TM3 cells transiently, with a noticeable heterogeneity of cellular responses.
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Affiliation(s)
- Wiktoria Kasprzycka
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Alicja Trębińska-Stryjewska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Rafał Bogdan Lewandowski
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Małgorzata Stępińska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Paulina Natalia Osuchowska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Monika Dobrzyńska
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Yahia Achour
- Faculty of Electronics, Military University of Technology, 00-908 Warsaw, Poland; (Y.A.); (J.S.)
| | - Łukasz Paweł Osuchowski
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Jacek Starzyński
- Faculty of Electronics, Military University of Technology, 00-908 Warsaw, Poland; (Y.A.); (J.S.)
| | - Zygmunt Mierczyk
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
| | - Elżbieta Anna Trafny
- Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, 00-908 Warsaw, Poland; (W.K.); (A.T.-S.); (R.B.L.); (M.S.); (P.N.O.); (M.D.); (Ł.P.O.); (Z.M.)
- Correspondence:
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22
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Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. Biomedicines 2021; 9:biomedicines9050582. [PMID: 34065451 PMCID: PMC8160971 DOI: 10.3390/biomedicines9050582] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 12/30/2022] Open
Abstract
Hypoxia is a condition in which cells, tissues, or organisms are deprived of sufficient oxygen supply. Aerobic organisms have a hypoxic response system, represented by hypoxia-inducible factor 1-α (HIF1A), to adapt to this condition. Due to publication bias, there has been little focus on genes other than well-known signature hypoxia-inducible genes. Therefore, in this study, we performed a meta-analysis to identify novel hypoxia-inducible genes. We searched publicly available transcriptome databases to obtain hypoxia-related experimental data, retrieved the metadata, and manually curated it. We selected the genes that are differentially expressed by hypoxic stimulation, and evaluated their relevance in hypoxia by performing enrichment analyses. Next, we performed a bibliometric analysis using gene2pubmed data to examine genes that have not been well studied in relation to hypoxia. Gene2pubmed data provides information about the relationship between genes and publications. We calculated and evaluated the number of reports and similarity coefficients of each gene to HIF1A, which is a representative gene in hypoxia studies. In this data-driven study, we report that several genes that were not known to be associated with hypoxia, including the G protein-coupled receptor 146 gene, are upregulated by hypoxic stimulation.
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23
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Nakamura T, Ogawa M, Kojima K, Takayanagi S, Ishihara S, Hattori K, Naguro I, Ichijo H. The mitochondrial Ca 2+ uptake regulator, MICU1, is involved in cold stress-induced ferroptosis. EMBO Rep 2021; 22:e51532. [PMID: 33822458 PMCID: PMC8097382 DOI: 10.15252/embr.202051532] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Ferroptosis has recently attracted much interest because of its relevance to human diseases such as cancer and ischemia-reperfusion injury. We have reported that prolonged severe cold stress induces lipid peroxidation-dependent ferroptosis, but the upstream mechanism remains unknown. Here, using genome-wide CRISPR screening, we found that a mitochondrial Ca2+ uptake regulator, mitochondrial calcium uptake 1 (MICU1), is required for generating lipid peroxide and subsequent ferroptosis under cold stress. Furthermore, the gatekeeping activity of MICU1 through mitochondrial calcium uniporter (MCU) is suggested to be indispensable for cold stress-induced ferroptosis. MICU1 is required for mitochondrial Ca2+ increase, hyperpolarization of the mitochondrial membrane potential (MMP), and subsequent lipid peroxidation under cold stress. Collectively, these findings suggest that the MICU1-dependent mitochondrial Ca2+ homeostasis-MMP hyperpolarization axis is involved in cold stress-induced lipid peroxidation and ferroptosis.
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Affiliation(s)
- Toshitaka Nakamura
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Motoyuki Ogawa
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Kazuki Kojima
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Saki Takayanagi
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Shunya Ishihara
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Kazuki Hattori
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Isao Naguro
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Hidenori Ichijo
- Laboratory of Cell SignalingGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
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24
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Giugliani R, Martins AM, So S, Yamamoto T, Yamaoka M, Ikeda T, Tanizawa K, Sonoda H, Schmidt M, Sato Y. Iduronate-2-sulfatase fused with anti-hTfR antibody, pabinafusp alfa, for MPS-II: A phase 2 trial in Brazil. Mol Ther 2021; 29:2378-2386. [PMID: 33781915 PMCID: PMC8261166 DOI: 10.1016/j.ymthe.2021.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/05/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
In Hunter syndrome (mucopolysaccharidosis II [MPS-II]), systemic accumulation of glycosaminoglycans (GAGs) due to a deficiency of iduronate-2-sulfatase (IDS), caused by mutations in the IDS gene, leads to multiple somatic manifestations and in patients with the severe (neuronopathic) phenotype, also to central nervous system (CNS) involvement. These symptoms cannot be effectively treated with current enzyme-replacement therapies, as they are unable to cross the blood-brain barrier (BBB). Pabinafusp alfa, a novel IDS fused with an anti-human transferrin receptor antibody, was shown to penetrate the BBB and to address neurodegeneration in preclinical studies. Subsequent phase 1/2 and 2/3 clinical studies in Japan have shown marked reduction of GAG accumulation in the cerebrospinal fluid (CSF), along with favorable clinical responses. A 26-week, open-label, randomized, parallel-group phase 2 study was conducted in Brazil to further evaluate the safety and efficacy of intravenously administered pabinafusp alfa at 1.0, 2.0, and 4.0 mg/kg/week in MPS-II patients. The safety profiles in the three dosage groups were similar. Neurodevelopmental evaluation suggested positive neurocognitive signals despite a relatively short study period. The 2.0-mg/kg group, which demonstrated marked reductions in substrate concentrations in the CSF, serum, and urine, was considered to provide the best combination regarding safety and efficacy signals.
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Affiliation(s)
- Roberto Giugliani
- Department of Genetics, UFRGS, and Medical Genetics Service, HCPA, Porto Alegre 90035-903, Brazil
| | - Ana Maria Martins
- Department of Pediatrics, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Sairei So
- JCR Pharmaceuticals, Ashiya 659-0021, Japan
| | | | | | | | | | | | | | - Yuji Sato
- JCR Pharmaceuticals, Ashiya 659-0021, Japan.
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25
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Nagayoshi Y, Chujo T, Hirata S, Nakatsuka H, Chen CW, Takakura M, Miyauchi K, Ikeuchi Y, Carlyle BC, Kitchen RR, Suzuki T, Katsuoka F, Yamamoto M, Goto Y, Tanaka M, Natsume K, Nairn AC, Suzuki T, Tomizawa K, Wei FY. Loss of Ftsj1 perturbs codon-specific translation efficiency in the brain and is associated with X-linked intellectual disability. SCIENCE ADVANCES 2021; 7:7/13/eabf3072. [PMID: 33771871 PMCID: PMC7997516 DOI: 10.1126/sciadv.abf3072] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/09/2021] [Indexed: 05/06/2023]
Abstract
FtsJ RNA 2'-O-methyltransferase 1 (FTSJ1) gene has been implicated in X-linked intellectual disability (XLID), but the molecular pathogenesis is unknown. We show that Ftsj1 is responsible for 2'-O-methylation of 11 species of cytosolic transfer RNAs (tRNAs) at the anticodon region, and these modifications are abolished in Ftsj1 knockout (KO) mice and XLID patient-derived cells. Loss of 2'-O-methylation in Ftsj1 KO mouse selectively reduced the steady-state level of tRNAPhe in the brain, resulting in a slow decoding at Phe codons. Ribosome profiling showed that translation efficiency is significantly reduced in a subset of genes that need to be efficiently translated to support synaptic organization and functions. Ftsj1 KO mice display immature synaptic morphology and aberrant synaptic plasticity, which are associated with anxiety-like and memory deficits. The data illuminate a fundamental role of tRNA modification in the brain through regulation of translation efficiency and provide mechanistic insights into FTSJ1-related XLID.
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Affiliation(s)
- Y Nagayoshi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - T Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - S Hirata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - H Nakatsuka
- Department of Human Intelligence Systems, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | - C-W Chen
- Laboratory for Protein Conformation Diseases, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - M Takakura
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - K Miyauchi
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Y Ikeuchi
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - B C Carlyle
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - R R Kitchen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - T Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - F Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - M Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Y Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neurology, NCNP, Tokyo 187-8551, Japan
| | - M Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - K Natsume
- Department of Human Intelligence Systems, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | - A C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - T Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - K Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
| | - F-Y Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
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26
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Nishimichi N, Tsujino K, Kanno K, Sentani K, Kobayashi T, Chayama K, Sheppard D, Yokosaki Y. Induced hepatic stellate cell integrin, α8β1, enhances cellular contractility and TGFβ activity in liver fibrosis. J Pathol 2021; 253:366-373. [PMID: 33433924 PMCID: PMC7986747 DOI: 10.1002/path.5618] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 01/08/2021] [Indexed: 02/04/2023]
Abstract
No effective therapy exists for fatal fibrosis. New therapeutic targets are needed for hepatic fibrosis because the incidence keeps increasing. The activation and differentiation of fibroblasts into myofibroblasts that causes excessive matrix deposition is central to fibrosis. Here, we investigated whether (and which) integrin receptors for matrix proteins activate hepatic stellate cells (HSCs). First, integrin α‐subunits were investigated systematically for their expression over the course of HSC activation and their distribution on fibroblasts and other systemic primary cells. The most upregulated in plate culture‐activated HSCs and specifically expressed across fibroblast linages was the α8 subunit. An anti‐α8 neutralizing mAb was evaluated in three different murine fibrosis models: for cytotoxic (CCl4 treatment), non‐alcoholic steatohepatitis‐associated and cholestatic fibrosis. In all models, pathology and fibrosis markers (hydroxyproline and α‐smooth muscle actin) were improved following the mAb injection. We also CCl4‐treated mice with inducible Itga8−/−; these mice were protected from increased hydroxyproline levels. Furthermore, ITGA8 was upregulated in specimens from 90 patients with liver fibrosis, indicating the relevance of our findings to liver fibrosis in people. Mechanistically, inhibition or ligand engagement of HSC α8 suppressed and enhanced myofibroblast differentiation, respectively, and HSC/fibroblast α8 activated latent TGFβ. Finally, integrin α8β1 potentially fulfils the growing need for anti‐fibrotic drugs and is an integrin not to be ignored. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Norihisa Nishimichi
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
| | - Kazuyuki Tsujino
- Lung Biology Center, Department of Medicine, Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Keishi Kanno
- General Internal Medicine, Hiroshima University Hospital, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Sentani
- Molecular Pathology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Kobayashi
- Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Chayama
- Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Dean Sheppard
- Lung Biology Center, Department of Medicine, Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Yasuyuki Yokosaki
- Integrin-Matrix Biomedical Science, Translational Research Center, Hiroshima University, Hiroshima, Japan
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27
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Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip CW, Ooi J, Tagami M, Hori F, Agrawal S, Hon C, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, de Hoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res 2021; 49:D892-D898. [PMID: 33211864 PMCID: PMC7779024 DOI: 10.1093/nar/gkaa1054] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 11/15/2022] Open
Abstract
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.
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Affiliation(s)
- Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jesicca Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jayson Harshbarger
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Atsushi Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Fumi Hori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuya Ikeda
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hiromasa Ono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hidemasa Bono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Karolinska Institutet, Stockholm, Sweden
| | - Masaki Kato
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Norio Kobayashi
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Jay Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Correspondence may also be addressed to Hideya Kawaji.
| | - Takeya Kasukawa
- To whom correspondence should be addressed. Tel: +81 45 503 9222; Fax: +81 45 503 9219;
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Yano T, Tsukita K, Kanoh H, Nakayama S, Kashihara H, Mizuno T, Tanaka H, Matsui T, Goto Y, Komatsubara A, Aoki K, Takahashi R, Tamura A, Tsukita S. A microtubule-LUZP1 association around tight junction promotes epithelial cell apical constriction. EMBO J 2021; 40:e104712. [PMID: 33346378 PMCID: PMC7809799 DOI: 10.15252/embj.2020104712] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 10/02/2020] [Accepted: 10/14/2020] [Indexed: 12/29/2022] Open
Abstract
Apical constriction is critical for epithelial morphogenesis, including neural tube formation. Vertebrate apical constriction is induced by di-phosphorylated myosin light chain (ppMLC)-driven contraction of actomyosin-based circumferential rings (CRs), also known as perijunctional actomyosin rings, around apical junctional complexes (AJCs), mainly consisting of tight junctions (TJs) and adherens junctions (AJs). Here, we revealed a ppMLC-triggered system at TJ-associated CRs for vertebrate apical constriction involving microtubules, LUZP1, and myosin phosphatase. We first identified LUZP1 via unbiased screening of microtubule-associated proteins in the AJC-enriched fraction. In cultured epithelial cells, LUZP1 was found localized at TJ-, but not at AJ-, associated CRs, and LUZP1 knockout resulted in apical constriction defects with a significant reduction in ppMLC levels within CRs. A series of assays revealed that ppMLC promotes the recruitment of LUZP1 to TJ-associated CRs, where LUZP1 spatiotemporally inhibits myosin phosphatase in a microtubule-facilitated manner. Our results uncovered a hitherto unknown microtubule-LUZP1 association at TJ-associated CRs that inhibits myosin phosphatase, contributing significantly to the understanding of vertebrate apical constriction.
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Affiliation(s)
- Tomoki Yano
- Laboratory of Biological ScienceGraduate School of MedicineOsaka UniversityOsakaJapan
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Kazuto Tsukita
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
- Department of NeurologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Hatsuho Kanoh
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
- Graduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Shogo Nakayama
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Hiroka Kashihara
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Tomoaki Mizuno
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Hiroo Tanaka
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
- Department of PharmacologySchool of MedicineTeikyo UniversityTokyoJapan
- Strategic Innovation and Research CenterTeikyo UniversityTokyoJapan
| | - Takeshi Matsui
- Laboratory for Skin HomeostasisResearch Center for Allergy and ImmunologyRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yuhei Goto
- Exploratory Research Center on Life and Living Systems (ExCELLS)National Institutes of Natural SciencesAichiJapan
- National Institute for Basic BiologyNational Institutes of Natural SciencesAichiJapan
- Department of Basic BiologyFaculty of Life ScienceSOKENDAI (Graduate University for Advanced Studies)AichiJapan
| | - Akira Komatsubara
- Exploratory Research Center on Life and Living Systems (ExCELLS)National Institutes of Natural SciencesAichiJapan
- National Institute for Basic BiologyNational Institutes of Natural SciencesAichiJapan
- Department of Basic BiologyFaculty of Life ScienceSOKENDAI (Graduate University for Advanced Studies)AichiJapan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems (ExCELLS)National Institutes of Natural SciencesAichiJapan
- National Institute for Basic BiologyNational Institutes of Natural SciencesAichiJapan
- Department of Basic BiologyFaculty of Life ScienceSOKENDAI (Graduate University for Advanced Studies)AichiJapan
| | - Ryosuke Takahashi
- Department of NeurologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Atsushi Tamura
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
- Department of PharmacologySchool of MedicineTeikyo UniversityTokyoJapan
- Strategic Innovation and Research CenterTeikyo UniversityTokyoJapan
| | - Sachiko Tsukita
- Laboratory of Barriology and Cell BiologyGraduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
- Strategic Innovation and Research CenterTeikyo UniversityTokyoJapan
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29
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Inoue Y, Okamoto T, Honda T, Nukui Y, Akashi T, Takemura T, Tozuka M, Miyazaki Y. Disruption in the balance between apolipoprotein A-I and mast cell chymase in chronic hypersensitivity pneumonitis. IMMUNITY INFLAMMATION AND DISEASE 2020; 8:659-671. [PMID: 33016012 PMCID: PMC7654418 DOI: 10.1002/iid3.355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Background Apolipoprotein A‐I (apoA‐I) has an antifibrotic effect in idiopathic pulmonary fibrosis. Although pulmonary fibrosis is associated with poor prognosis of patients with hypersensitivity pneumonitis (HP), little is known regarding the role of apoA‐I in the pathogenesis of HP. Methods Two‐dimensional electrophoresis, immunoblotting, and enzyme‐linked immunosorbent assays were performed for the identification and quantification of apoA‐I in bronchoalveolar lavage fluid (BALF) from patients with acute and chronic HP. To investigate the degradation of apoA‐I, apoA‐I was incubated with BALF. Moreover, the role of apoA‐I in TGF‐β1‐induced epithelial–mesenchymal transition of A549 cells was examined. Results The concentration of apoA‐I in the BALF was significantly lower in chronic HP (n = 56) compared with acute HP (n = 31). The expression level of apoA‐I was also low in the lung tissues of chronic HP. ApoA‐I was degraded by BALF from HP patients. The number of chymase‐positive mast cells in the alveolar parenchyma was inversely correlated with apoA‐I levels in the BALF of chronic HP patients. In vitro experiment using A549 cells, untreated apoA‐I inhibited TGF‐β1‐induced epithelial–mesenchymal transition, although this trend was not observed in the chymase‐treated apoA‐I. Conclusions A decrease of apoA‐I was associated with the pathogenesis of chronic HP in terms of pulmonary fibrosis and mast cell chymase attenuated the protective effect of apoA‐I against pulmonary fibrosis. Furthermore, apoA‐I could be a crucial molecule associated with lung fibrogenesis of HP.
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Affiliation(s)
- Yukihisa Inoue
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tsukasa Okamoto
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihisa Nukui
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takumi Akashi
- Department of Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tamiko Takemura
- Department of Pathology, Japan Red Cross Centre, Tokyo, Japan
| | - Minoru Tozuka
- Department of Analytical Laboratory Chemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
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30
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Identification of GLUT12/SLC2A12 as a urate transporter that regulates the blood urate level in hyperuricemia model mice. Proc Natl Acad Sci U S A 2020; 117:18175-18177. [PMID: 32690690 PMCID: PMC7414087 DOI: 10.1073/pnas.2006958117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent genome-wide association studies have revealed some genetic loci associated with serum uric acid levels and susceptibility to gout/hyperuricemia which contain potential candidates of physiologically important urate transporters. One of these novel loci is located upstream of SGK1 and SLC2A12, suggesting that variations in these genes increase the risks of hyperuricemia and gout. We herein focused on SLC2A12 encoding a transporter, GLUT12, the physiological function of which remains unclear. As GLUT12 belongs to the same protein family as a well-recognized urate transporter GLUT9, we hypothesized that GLUT12 mediates membrane transport of urate. Therefore, we conducted functional assays and analyzed Glut12 knockout hyperuricemia model mice, generated using the CRISPR-Cas9 system. Our results revealed that GLUT12 acts as a physiological urate transporter and its dysfunction elevates the blood urate concentration. This study provides insights into the deeper understanding of the urate regulatory system in the body, which is also important for pathophysiology of gout/hyperuricemia.
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31
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Kimura M, Horie T, Baba O, Ide Y, Tsuji S, Ruiz Rodriguez R, Watanabe T, Yamasaki T, Otani C, Xu S, Miyasaka Y, Nakashima Y, Kimura T, Ono K. Homeobox A4 suppresses vascular remodeling by repressing YAP/TEAD transcriptional activity. EMBO Rep 2020; 21:e48389. [PMID: 32147946 PMCID: PMC7132199 DOI: 10.15252/embr.201948389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
The Hippo signaling pathway is involved in the pathophysiology of various cardiovascular diseases. Yes-associated protein (YAP) and transcriptional enhancer activator domain (TEAD) transcriptional factors, the main transcriptional complex of the Hippo pathway, were recently identified as modulators of phenotypic switching of vascular smooth muscle cells (VSMCs). However, the intrinsic regulator of YAP/TEAD-mediated gene expressions involved in vascular pathophysiology remains to be elucidated. Here, we identified Homeobox A4 (HOXA4) as a potent repressor of YAP/TEAD transcriptional activity using lentiviral shRNA screen. Mechanistically, HOXA4 interacts with TEADs and attenuates YAP/TEAD-mediated transcription by competing with YAP for TEAD binding. We also clarified that the expression of HOXA4 is relatively abundant in the vasculature, especially in VSMCs. In vitro experiments in human VSMCs showed HOXA4 maintains the differentiation state of VSMCs via inhibition of YAP/TEAD-induced phenotypic switching. We generated Hoxa4-deficient mice and confirmed the downregulation of smooth muscle-specific contractile genes and the exacerbation of vascular remodeling after carotid artery ligation in vivo. Our results demonstrate that HOXA4 is a repressor of VSMC phenotypic switching by inhibiting YAP/TEAD-mediated transcription.
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Affiliation(s)
- Masahiro Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Horie
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Baba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuya Ide
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuhei Tsuji
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Randolph Ruiz Rodriguez
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshimitsu Watanabe
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Yamasaki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chiharu Otani
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sijia Xu
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yui Miyasaka
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Nakashima
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koh Ono
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Bono H. All of gene expression (AOE): An integrated index for public gene expression databases. PLoS One 2020; 15:e0227076. [PMID: 31978081 PMCID: PMC6980531 DOI: 10.1371/journal.pone.0227076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022] Open
Abstract
Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.
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Affiliation(s)
- Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima,Japan
- * E-mail:
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Miyamoto-Mikami E, Miyamoto N, Kumagai H, Hirata K, Kikuchi N, Zempo H, Kimura N, Kamiya N, Kanehisa H, Naito H, Fuku N. COL5A1 rs12722 polymorphism is not associated with passive muscle stiffness and sports-related muscle injury in Japanese athletes. BMC MEDICAL GENETICS 2019; 20:192. [PMID: 31791263 PMCID: PMC6889657 DOI: 10.1186/s12881-019-0928-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 11/20/2019] [Indexed: 08/30/2023]
Abstract
BACKGROUND Poor joint flexibility has been repeatedly proposed as a risk factor for muscle injury. The C-to-T polymorphism (rs12722) in the 3'-untranslated region of the collagen type V α1 chain gene (COL5A1) is reportedly associated with joint flexibility. Flexibility of a normal joint is largely determined by passive muscle stiffness, which is influenced by intramuscular collagenous connective tissues including type V collagen. The present study aimed to test the hypothesis that the COL5A1 rs12722 polymorphism influences joint flexibility via passive muscle stiffness, and is accordingly associated with the incidence of muscle injury. METHODS In Study 1, we examined whether the rs12722 polymorphism is associated with joint flexibility and passive muscle stiffness in 363 healthy young adults. Joint flexibility was evaluated by passive straight-leg-raise and sit-and-reach tests, and passive muscle stiffness was measured using ultrasound shear wave elastography. In Study 2, the association of the rs12722 polymorphism with sports-related muscle injury was assessed in 1559 Japanese athletes. Muscle injury history and severity were assessed by a questionnaire. In both Study 1 and Study 2, the rs12722 C-to-T polymorphism in the COL5A1 was determined using the TaqMan SNP Genotyping Assay. RESULTS Study 1 revealed that the rs12722 polymorphism had no significant effect on range of motion in passive straight-leg-raise and sit-and-reach tests. Furthermore, there was no significant difference in passive muscle stiffness of the hamstring among the rs12722 genotypes. In Study 2, rs12722 genotype frequencies did not differ between the muscle injury and no muscle injury groups. Moreover, no association was observed between rs12722 polymorphism and severity of muscle injury. CONCLUSIONS The present study does not support the view that COL5A1 rs12722 polymorphism has a role as a risk factor for sports-related muscle injury, or that it is a determinant for passive muscle stiffness in a Japanese population.
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Affiliation(s)
- Eri Miyamoto-Mikami
- Institute of Health and Sports Science & Medicine, Juntendo University, 1-1 Hiraka-gakuendai, Inzai City, Chiba, 270-1695, Japan. .,Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan.
| | - Naokazu Miyamoto
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Hiroshi Kumagai
- Institute of Health and Sports Science & Medicine, Juntendo University, 1-1 Hiraka-gakuendai, Inzai City, Chiba, 270-1695, Japan.,Research Fellow of Japanese Society for the Promotion of Science, Tokyo, Japan
| | - Kosuke Hirata
- Research Fellow of Japanese Society for the Promotion of Science, Tokyo, Japan.,Graduate School of Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
| | - Naoki Kikuchi
- Department of Training Science, Nippon Sport Science University, Tokyo, Japan
| | - Hirofumi Zempo
- Institute of Health and Sports Science & Medicine, Juntendo University, 1-1 Hiraka-gakuendai, Inzai City, Chiba, 270-1695, Japan.,Faculty of Health and Nutrition, Tokyo Seiei College, Tokyo, Japan
| | - Noriko Kimura
- Graduate School of Sport and Exercise Sciences, Osaka University of Health and Sport Sciences, Osaka, Japan
| | - Nobuhiro Kamiya
- Faculty of Budo and Sport Studies, Tenri University, Nara, Japan
| | - Hiroaki Kanehisa
- Faculty of Sport and Health Science, Ritsumeikan University, Shiga, Japan
| | - Hisashi Naito
- Institute of Health and Sports Science & Medicine, Juntendo University, 1-1 Hiraka-gakuendai, Inzai City, Chiba, 270-1695, Japan.,Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan.,Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Noriyuki Fuku
- Institute of Health and Sports Science & Medicine, Juntendo University, 1-1 Hiraka-gakuendai, Inzai City, Chiba, 270-1695, Japan.,Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan.,Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
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Ichino F, Bono H, Nakazato T, Toyoda A, Fujiyama A, Iwabuchi K, Sato R, Tabunoki H. Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae. Drug Discov Ther 2019; 12:7-15. [PMID: 29553084 DOI: 10.5582/ddt.2018.01004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human intestinal absorption is estimated using a human colon carcinoma cell line (Caco-2) cells from human colorectal adenocarcinoma, intestinal perfusion, or a mammalian model. These current evaluation systems are limited in their ability to estimate human intestinal absorption. In addition, in vivo evaluation systems using laboratory animals such as mice and rats entail animal ethics problems, and it is difficult to screen compounds on a large scale at the drug discovery stage. Thus, we propose the use of Bombyx mori larvae for evaluation of intestinal absorption of compounds as an alternative system in this study. First, to compare the characteristics among Caco-2 cells, human intestine, and B. mori larval midgut, we analyzed their RNA-seq data, and we found 26 drug transporters common to humans and B. mori. Next, we quantitatively developed an oral administration technique in B. mori and established a method using silkworm B. mori larvae that can easily estimate the intestinal permeability of compounds. Consequently, we could determine the dose and technique for oral administration in B. mori larvae. We also developed a B. mori model to evaluate the intestinal permeability of orally administered. Our constructed evaluation system will be useful for evaluating intestinal permeability in medical drug development.
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Affiliation(s)
- Fumika Ichino
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS)
| | - Takeru Nakazato
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS)
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics
| | - Kikuo Iwabuchi
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
| | - Ryoichi Sato
- Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology
| | - Hiroko Tabunoki
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology
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35
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Yasunaga M, Saijou S, Hanaoka S, Anzai T, Tsumura R, Matsumura Y. Significant antitumor effect of an antibody against TMEM180, a new colorectal cancer-specific molecule. Cancer Sci 2019; 110:761-770. [PMID: 30537002 PMCID: PMC6361608 DOI: 10.1111/cas.13907] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
The present state of therapy for colorectal cancer (CRC) is far from satisfactory, highlighting the need for new targets for this disease. We identified a new CRC‐specific molecule, TMEM180, a predicted 11‐pass transmembrane protein that apparently functions as a cation symporter. We developed an anti‐TMEM180 mAb and then succeeded in humanizing the mAb. Immunohistochemistry (IHC) in CRC with the mAb showed a similar positivity rate as compared with anti‐epidermal growth factor receptor mAb, and IHC with anti‐TMEM180 mAb did not show staining in major organs used in this study. Immune electron microscopy clearly indicated that TMEM180 was present on the tumor exosome. The TMEM180 promoter region contains 10 hypoxia‐responsive element consensus sequences; accordingly, SW480 cells upregulated TMEM180 under low‐oxygen conditions. Anti‐TMEM180 mAb has in vitro antibody‐dependent cell‐mediated cytotoxicity and complement‐dependent cytotoxicity activity, and SW480 CRC xenografts were eradicated by the mAb. These data indicate that TMEM180 may be a new CRC marker and that a mAb against this protein could be used as antibody‐based therapy against CRC.
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Affiliation(s)
- Masahiro Yasunaga
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
| | - Shinji Saijou
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
| | - Shingo Hanaoka
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
| | - Takahiro Anzai
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
| | - Ryo Tsumura
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Exploratory Oncology Research & Clinical Trial Centre, National Cancer Centre, Kashiwa, Japan
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Asai A, Koseki J, Konno M, Nishimura T, Gotoh N, Satoh T, Doki Y, Mori M, Ishii H. Drug discovery of anticancer drugs targeting methylenetetrahydrofolate dehydrogenase 2. Heliyon 2018; 4:e01021. [PMID: 30582043 PMCID: PMC6299143 DOI: 10.1016/j.heliyon.2018.e01021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/10/2018] [Accepted: 12/04/2018] [Indexed: 01/07/2023] Open
Abstract
Many anticancer drugs have serious adverse effects; therefore, it is necessary to target features specific to cancer cells to minimize the effects on healthy cells. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) was reported to be specifically enhanced in cancer. We confirmed the validity of MTHFD2 as a drug discovery target using clinical data. In addition, we performed in silico screening to design an anticancer drug specifically targeting MTHFD2. Analysis of the clinical data indicated that MTHFD2 was enhanced in most cancers compared with normal tissues, and affected the prognosis in cancer patients. Candidate compounds for MTHFD2 inhibitors were identified using in silico drug discovery techniques, and the important interactions for MTHFD2 binding were determined. In addition, these candidate compounds decreased levels of MTHFD2 metabolites in cancer cells. The findings of the present study may help to develop anticancer drugs targeting MTHFD2, with a view to minimizing the adverse effects of anticancer drugs.
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Affiliation(s)
- Ayumu Asai
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Gastroenterological Surgery Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Jun Koseki
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Tatsunori Nishimura
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Noriko Gotoh
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Taroh Satoh
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Yuichiro Doki
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Gastroenterological Surgery Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
| | - Masaki Mori
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Gastroenterological Surgery Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan
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37
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Clarkson MD, Whipple ME. Variation in the representation of human anatomy within digital resources: Implications for data integration. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2018:330-339. [PMID: 30815072 PMCID: PMC6371295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Clinical informatics makes use of anatomical representation-particularly in the form of anatomical terms. But differences and ambiguities in naming anatomical structures and partitioning the body can complicate efforts to interlink anatomical resources and integrate clinical data. To better understand differences in representations of human anatomy, we compare five digital resources: a formal ontology, a terminology, and three 3D graphics applications. Because the graphics applications offer explicit representation of the boundaries and partitions of anatomical structures, they reveal the differences in modeling of anatomy that may not be apparent through text-based representations. The variations in these resources allow us to categorize differences in representations of anatomy and to highlight the importance of this topic in the context of clinical informatics.
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Affiliation(s)
- Melissa D Clarkson
- Division of Biomedical Informatics, University of Kentucky, Lexington, KY
| | - Mark E Whipple
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA
- Department of Otolaryngology-Head and Neck Surgery, University of Washington, Seattle, WA
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38
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Nakashima Y, Miyagi-Shiohira C, Noguchi H, Omasa T. The Healing Effect of Human Milk Fat Globule-EGF Factor 8 Protein (MFG-E8) in A Rat Model of Parkinson's Disease. Brain Sci 2018; 8:brainsci8090167. [PMID: 30200351 PMCID: PMC6162645 DOI: 10.3390/brainsci8090167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/21/2022] Open
Abstract
We searched for drugs that alleviate the reduction of dopaminergic neurons caused by the administration of lipopolysaccharide (LPS) to the substantia nigra of the rat brain. Human milk fat globule-EGF factor 8 protein (MFG-E8) is similar to MFG-E8-S, a short isoform, of the mouse MFG-E8. However, the function of MFG-E8-S was not clear. Rats with LPS-induced Parkinson’s disease were prepared and the effects of human MFG-E8 were examined. MFG-E8 improved the significant reduction in mesencephalic dopamine neurons induced by the administration of LPS. LPS was administered to human induced pluripotent stem cell (iPSC)-derived dopaminergic neurons to induce inflammation and the effect of MFG-E8 was examined. MFG-E8 showed no toxicity toward neurons. We reanalyzed the results using public microarray data. MFG-E8 mRNA was found to be expressed in all parts of the body, particularly by adipose-derived stem cells (ADSCs). Furthermore, we investigated the culture supernatant of ADSCs using the liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis method and successfully identified the peptide of the MFG-E8 F5/8 type C domain. The results suggested that MFG-E8-S may have a preventive effect against Parkinson’s disease.
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Affiliation(s)
- Yoshiki Nakashima
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.
| | - Chika Miyagi-Shiohira
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.
| | - Hirofumi Noguchi
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.
| | - Takeshi Omasa
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan.
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39
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Unbiased compound screening with a reporter gene assay highlights the role of p13 in the cardiac cellular stress response. Biochem Biophys Res Commun 2018; 495:1992-1997. [PMID: 29180011 DOI: 10.1016/j.bbrc.2017.11.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/18/2017] [Indexed: 11/20/2022]
Abstract
We recently showed that a 13-kDa protein (p13), the homolog protein of formation of mitochondrial complex V assembly factor 1 in yeast, acts as a potential protective factor in pancreatic islets under diabetes. Here, we aimed to identify known compounds regulating p13 mRNA expression to obtain therapeutic insight into the cellular stress response. A luciferase reporter system was developed using the putative promoter region of the human p13 gene. Overexpression of peroxisome proliferator-activated receptor gamma coactivator 1α, a master player regulating mitochondrial metabolism, increased both reporter activity and p13 expression. Following unbiased screening with 2320 known compounds in HeLa cells, 12 pharmacological agents (including 8 cardiotonics and 2 anthracyclines) that elicited >2-fold changes in p13 mRNA expression were identified. Among them, four cardiac glycosides decreased p13 expression and concomitantly elevated cellular oxidative stress. Additional database analyses showed highest p13 expression in heart, with typically decreased expression in cardiac disease. Accordingly, our results illustrate the usefulness of unbiased compound screening as a method for identifying novel functional roles of unfamiliar genes. Our findings also highlight the importance of p13 in the cellular stress response in heart.
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Kawashima S, Katayama T, Hatanaka H, Kushida T, Takagi T. NBDC RDF portal: a comprehensive repository for semantic data in life sciences. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5255118. [PMID: 30576482 PMCID: PMC6301334 DOI: 10.1093/database/bay123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/15/2018] [Indexed: 11/28/2022]
Abstract
In the life sciences, researchers increasingly want to access multiple databases in an integrated way. However, different databases currently use different formats and vocabularies, hindering the proper integration of heterogeneous life science data. Adopting the Resource Description Framework (RDF) has the potential to address such issues by improving database interoperability, leading to advances in automatic data processing. Based on this idea, we have advised many Japanese database development groups to expose their databases in RDF. To further promote such activities, we have developed an RDF-based life science dataset repository called the National Bioscience Database Center (NBDC) RDF portal. All the datasets in this repository have been reviewed by the NBDC to ensure interoperability and queryability. As of July 2018, the service includes 21 RDF datasets, comprising over 45.5 billion triples. It provides SPARQL endpoints for all datasets, useful metadata and the ability to download RDF files. The NBDC RDF portal can be accessed at https://integbio.jp/rdf/.
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Affiliation(s)
- Shuichi Kawashima
- Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, Japan
| | - Toshiaki Katayama
- Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, Japan
| | - Hideki Hatanaka
- National Bioscience Database Center, Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo, Japan
| | - Tatsuya Kushida
- National Bioscience Database Center, Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo, Japan
| | - Toshihisa Takagi
- National Bioscience Database Center, Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo, Japan.,DNA Data Bank of Japan Center, National Institute of Genetics, Shizuoka, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, Japan
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