Papers - Arita, Makoto

Maternal gut microbiota in pregnancy influences offspring metabolic phenotype.

Kimura I, Miyamoto J, Ohue-Kitano R, Watanabe K, Yamada T, Onuki M, Aoki R, Isobe Y, Kashihara D, Inoue D, Inaba A, Takamura Y, Taira S, Kumaki S, Watanabe M, Ito M, Nakagawa F, Irie J, Kakuta H, Shinohara M, Iwatsuki K, Tsujimoto G, Ohno H, Arita M, Itoh H, Hase K.

Science 367   eaaw8429 2020.02

Research paper (scientific journal), Joint Work, Accepted

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Maternal ω3 docosapentaenoic acid inhibits infant allergic dermatitis through TRAIL-expressing plasmacytoid dendritic cells in mice.

Hirata SI, Nagatake T, Sawane K, Hosomi K, Honda T, Ono S, Ikeda K, Aoyagi R, Adachi J, Abe Y, Isoyama J, Suzuki H, Tomonaga T, Kiyono H, Kabashima K, Arita M, Kunisawa J.

Allergy 75   1935 - 1951 2020.02

Research paper (scientific journal), Joint Work, Accepted

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Homeistatic function of dermokine in the skin barrier and inflammation.

Utsunomiya A, Chino T, Utsunomiya N, Luong VH, Tokuriki A, Naganuma T, Arita M, Higashi K, Saito K, Suzuki N, Ohara A, Sugai M, Sugawara K, Tsuruta D, Oyama N, Hasegawa M.

J Invest Dermatol 140   838 - 849 2020

Research paper (scientific journal), Joint Work, Accepted

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Acyl-CoA synthetase 6 regulates long chain polyunsaturated fatty acid composition of membrane phospholipids in spermatids and supports normal spermatogenic processes in mice.

Shishikura K, Kuroha S, Matsueda S, Iseki H, Matsui T, Inoue A, Arita M.

FASEB J  33 ( 12 ) 14194 - 14203 2019.12

Research paper (scientific journal), Joint Work, Accepted

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Dietary omega-3 fatty acid ameliorates allergic rhinitis via eosinophilic production of the anti-allergic lipid mediator 15-hydroxyeicosapentaenoic acid in mice.

Sawane K, Nagatake T, Hosomi K, Hirata S, Adachi J, Abe Y, Isoyama J, Suzuki H, Matsunaga A, Fukumitsu S, Aida K, Tomonaga T, Arita M, Kunisawa J.

Nutrients 11   2868 2019.11

Research paper (scientific journal), Joint Work, Accepted

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Bi-directional crosstalk between neutrophils and adipocytes promotes adipose tissue inflammation.

Watanabe Y, Nagai Y, Honda H, Okamoto N, Yanagibashi T, Ogasawara M, Yamamoto S, Imamura R, Takasaki I, Hara H, Sasahara M, Arita M, Hida S, Taniguchi S, Suda T, Takatsu K.

FASEB J  33 ( 11 ) 11821 - 11835 2019.11

Research paper (scientific journal), Joint Work, Accepted

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Characterization of lipid profiles after dietary intake of polyunsaturated fatty acids using integrated untargeted and targeted lipidomics.

Naoe S, Tsugawa H, Takahashi M, Ikeda K, Arita M.

Metabolites 9   241 2019.10

Research paper (scientific journal), Joint Work, Accepted

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Gut microbiota confers host resistance to obesity by metabolizing dietary polyunsaturated fatty acids.

Miyamoto J, Igarashi M, Watanabe K, Karaki SI, Mukouyama H, Kishino S, Li X, Ichimura A, Irie J, Sugimoto Y, Mizutani T, Sugawara T, Miki T, Ogawa J, Drucker DJ, Arita M, Itoh H, Kimura I.

Nature Communications 10 ( 1 ) 4007 2019.09

Research paper (scientific journal), Joint Work, Accepted

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Preferential incorporation of administered eicosapentaenoic acid into thin-cap atherosclerotic plaques.

Sato T, Horikawa M, Takei S, Yamazaki F, Ito TK, Kondo T, Sakurai T, Kahyo T, Ikegami K, Sato S, Sato R, Jinno Y, Kawano H, Naoe S, Arita M, Kashiwagi Y, Setou M.

Arterioscler Thromb Vasc Biol 39 ( 9 ) 1802 - 1816 2019.09

Research paper (scientific journal), Joint Work, Accepted

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Dysregulated fatty acid metabolism in nasal polyp-derived eosinophils from patients with chronic rhinosinusitis

Miyata J., Fukunaga K., Kawashima Y., Watanabe T., Saitoh A., Hirosaki T., Araki Y., Kikawada T., Betsuyaku T., Ohara O., *Arita M.

Allergy: European Journal of Allergy and Clinical Immunology (Allergy: European Journal of Allergy and Clinical Immunology)  74 ( 6 ) 1113 - 1124 2019.06

Research paper (scientific journal), Joint Work, Accepted,  ISSN  01054538

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© 2019 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd. Background: Eosinophils are multifunctional granulocytes capable of releasing various cytokines, chemokines, and lipid mediators. We previously reported dysregulated fatty acid metabolism in peripheral blood-derived eosinophils from patients with severe asthma. However, functional characteristics of eosinophils present in allergic inflammatory tissues remain largely uncharacterized. Methods: We established a method for isolating CD69hi CCR3low CXCR4- siglec-8int eosinophils from nasal polyps of patients with eosinophilic rhinosinusitis (NP-EOS). Multi-omics analysis including lipidomics, proteomics, and transcriptomics was performed to analyze NP-EOS as compared to peripheral blood-derived eosinophils from healthy subjects (PB-EOS). Results: Lipidomic analysis revealed impaired synthesis of prostaglandins and 15-lipoxygenase (15-LOX)-derived mediators, and selective upregulation of leukotriene D4 production. Furthermore, proteomics and transcriptomics revealed changes in the expression of specific enzymes (GGT5, DPEP2, and 15-LOX) responsible for dysregulated lipid metabolism. Ingenuity pathway analysis indicated the importance of type 2 cytokines and pattern recognition receptor pathways. Stimulation of PB-EOS with eosinophil activators IL-5, GM-CSF, and agonists of TLR2 and NOD2 mimicked the observed changes in lipid metabolism. Conclusion: Inflammatory tissue-derived eosinophils possess a specific phenotype with dysregulated fatty acid metabolism that may be targeted therapeutically to control eosinophilic inflammatory diseases.

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Proteogenomic Analyses of Cellular Lysates Using a Phenol-Guanidinium Thiocyanate Reagent

Kawashima Y., Miyata J., Watanabe T., Shioya J., Arita M., Ohara O.

Journal of Proteome Research (Journal of Proteome Research)  18 ( 1 ) 301 - 308 2019.01

Research paper (scientific journal), Joint Work, Accepted,  ISSN  15353893

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© Copyright 2018 American Chemical Society. Protein and RNA profiles are highly informative when generating a comprehensive understanding of the dynamics of complex biological systems. Quantitative correlations between protein and RNA profiles are not always high, yet simultaneous acquisition of both profiles remains challenging, in part because of the limited availability of samples and the inconvenience of separately preparing protein and RNA fractions. In a previous study, protein, DNA, and RNA fractions were simultaneously prepared from the same sample using phenol-guanidinium isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts in proteogenomic analyses remains poorly understood. We therefore evaluated the performance of the P/GTC-extraction method in proteogenomic analyses using standard HEK293-F cells and human peripheral blood neutrophils. The latter cell type is renowned for its extreme vulnerability to protein/RNA degradation, reflecting high protease and RNase activities. Our data indicate that the P/GTC extraction method provides superior protein profiles from neutrophil and HEK293-F cell samples for simultaneous preparation of RNA and protein, as compared with those from conventional protein extraction methods. The P/GTC extraction method therefore provides a powerful and robust tool for a broad range of proteogenomic studies.

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Reciprocal regulation of STING and TCR signaling by mTORC1 for T-cell activation and function

Imanishi T., Unno M., Kobayashi W., Yoneda N., Matsuda S., Ikeda K., Hoshii T., Hirao A., Miyake K., Barber G., Arita M., Ishii K., Akira S., Saito T.

Life Science Alliance (Life Science Alliance)  2 ( 1 ) e201800282 2019

Research paper (scientific journal), Joint Work, Accepted

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© 2019 Imanishi et al. Stimulator of interferon genes (STING) plays a key role in detecting cytosolic DNA and induces type I interferon (IFN-I) responses for host defense against pathogens. Although T cells highly express STING, its physiological role remains unknown. Here, we show that costimulation of T cells with the STING ligand cGAMP and TCR leads to IFN-I production and strongly inhibits T-cell growth. TCR-mediated mTORC1 activation and sustained activation of IRF3 are required for cGAMP-induced IFN-I production, and the mTORC1 activity is partially counteracted by cGAMP, thereby blocking proliferation. This mTORC1 inhibition in response to costimulation depends on IRF3 and IRF7. Effector T cells produce much higher IFN-I levels than innate cells in response to cGAMP. Finally, we demonstrated that STING stimulation in T cells is effective in inducing antitumor responses in vivo. Our studies demonstrate that the outputs of STING and TCR signaling pathways are mutually regulated through mTORC1 to modulate T-cell functions.

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Mass spectrometry data repository enhances novel metabolite discoveries with advances in computational metabolomics

Tsugawa H., Satoh A., Uchino H., Cajka T., Arita M., Arita M.

Metabolites (Metabolites)  9 ( 6 ) E119 2019

Research paper (scientific journal), Joint Work, Accepted

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© 2019 Metabolites. All rights reserved. Mass spectrometry raw data repositories, including Metabolomics Workbench and MetaboLights, have contributed to increased transparency in metabolomics studies and the discovery of novel insights in biology by reanalysis with updated computational metabolomics tools. Herein, we reanalyzed the previously published lipidomics data from nine algal species, resulting in the annotation of 1437 lipids achieving a 40% increase in annotation compared to the previous results. Specifically, diacylglyceryl-carboxyhydroxy-methylcholine (DGCC) in Pavlova lutheri and Pleurochrysis carterae, glucuronosyldiacylglycerol (GlcADG) in Euglena gracilis, and P. carterae, phosphatidylmethanol (PMeOH) in E. gracilis, and several oxidized phospholipids (oxidized phosphatidylcholine, OxPC; phosphatidylethanolamine, OxPE; phosphatidylglycerol, OxPG; phosphatidylinositol, OxPI) in Chlorella variabilis were newly characterized with the enriched lipid spectral databases. Moreover, we integrated the data from untargeted and targeted analyses from data independent tandem mass spectrometry (DIA-MS/MS) acquisition, specifically the sequential window acquisition of all theoretical fragment-ion MS/MS (SWATH-MS/MS) spectra, to increase the lipidomic annotation coverage. After the creation of a global library of precursor and diagnostic ions of lipids by the MS-DIAL untargeted analysis, the co-eluted DIA-MS/MS spectra were resolved in MRMPROBS targeted analysis by tracing the specific product ions involved in acyl chain compositions. Our results indicated that the metabolite quantifications based on DIA-MS/MS chromatograms were somewhat inferior to the MS1-centric quantifications, while the annotation coverage outperformed those of the untargeted analysis of the data dependent and DIA-MS/MS data. Consequently, integrated analyses of untargeted and targeted approaches are necessary to extract the maximum amount of metabolome information, and our results showcase the value of data repositories for the discovery of novel insights in lipid biology.

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Resolvin D1 enhances the resolution of lung inflammation caused by long-term Pseudomonas aeruginosa infection.

Codagnone M, Cianci E, Lamolinara A, Cecilia Mari V, Nespoli A, Arita M, Bragonzi A, Iezzi M, Romano M, *Recchiuti A.

Mucosal Immunol (Mucosal Immunology)  11 ( 1 ) 35 - 49 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  19330219

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Pseudomonas aeruginosa lung infection is a main cause of disability and mortality worldwide. Acute inflammation and its timely resolution are crucial for ensuring bacterial clearance and limiting tissue damage. Here, we investigated protective actions of resolvin (Rv) D1 in lung infection induced by the RP73 clinical strain of P. aeruginosa. RvD1 significantly diminished bacterial growth and neutrophil infiltration during acute pneumonia caused by RP73. Inoculum of RP73, immobilized in agar beads, resulted in persistent lung infection up to 21 days, leading to a non resolving inflammation reminiscent of human pathology. RvD1 significantly reduced bacterial titer, leukocyte infiltration, and lung tissue damage. In murine lung macrophages sorted during P. aeruginosa chronic infection, RvD1 regulated the expression of Toll-like receptors, downstream genes, and microRNA (miR)-21 and 155, resulting in reduced inflammatory signaling. In vitro, RvD1 enhanced phagocytosis of P. aeruginosa by neutrophils and macrophages, recapitulating its in vivo actions. These results unveil protective functions and mechanisms of action of RvD1 in acute and chronic P. aeruginosa pneumonia, providing evidence for its potent pro-resolution and tissue protective properties on airway mucosal tissue during infection.

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12-OH-17,18-epoxyeicosatetraenoic acid alleviates eosinophilic airway inflammation in murine lungs.

Mochimaru T, *Fukunaga K, Miyata J, Matsusaka M, Masaki K, Kabata H, Ueda S, Suzuki Y, Goto T, Urabe D, Inoue M, Isobe Y, Arita M, Betsuyaku T.

Allergy (Allergy: European Journal of Allergy and Clinical Immunology)  73 ( 2 ) 369 - 378 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  01054538

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© 2017 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd. Background: Asthma is characterized by airway inflammation and obstruction with eosinophil infiltration into the airway. Arachidonic acid, an omega-6 fatty acid, is metabolized into cysteinyl leukotriene with pro-inflammatory properties for allergic inflammation, whereas the omega-3 fatty acid eicosapentaenoic acid (EPA) and its downstream metabolites are known to have anti-inflammatory effects. In this study, we investigated the mechanism underlying the counter-regulatory roles of EPA in inflamed lungs. Methods: Male C57BL6 mice were sensitized and challenged by ovalbumin (OVA). After EPA treatment, we evaluated the cell count of Bronchoalveolar lavage fluid (BALF), mRNA expressions in the lungs by q-PCR, and the amounts of lipid mediators by liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics. We investigated the effect of the metabolite of EPA by in vivo and in vitro studies. Results: Eicosapentaenoic acid treatment reduced the accumulation of eosinophils in the airway and decreased mRNA expression of selected inflammatory mediators in the lung. Lipidomics clarified the metabolomic profile in the lungs. Among EPA-derived metabolites, 12-hydroxy-17,18-epoxyeicosatetraenoic acid (12-OH-17,18-EpETE) was identified as one of the major biosynthesized molecules; the production of this molecule was amplified by EPA administration and allergic inflammation. Intravenous administration of 12-OH-17,18-EpETE attenuated airway eosinophilic inflammation through downregulation of C-C chemokine motif 11 (CCL11) mRNA expression in the lungs. In vitro, this molecule also inhibited the release of CCL11 from human airway epithelial cells stimulated with interleukin-4. Conclusion: These results demonstrated that EPA alleviated airway eosinophilic inflammation through its conversion into bioactive metabolites. Additionally, our results suggest that 12-OH-17,18-EpETE is a potential therapeutic target for the management of asthma.

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Stereoselective total synthesis of macrophage-produced prohealing 14,21-dihydroxydocosahexaenoic acids.

Nishimura K, Sakaguchi T, Nanba Y, Suganuma Y, Morita M, Hong S, Lu Y, Jun B, Bazan NG, Arita M, *Kobayashi Y.

J Org Chem (Journal of Organic Chemistry)  83 ( 1 ) 154 - 166 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  00223263

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© 2017 American Chemical Society. Synthesis of 14S,21R- and 14S,21S-dihydroxy-DHA (diHDHA) among the four possible stereoisomers of 14,21-diHDHA was studied. Methyl (R)-lactate (>97% ee), selected as a C20-C22 fragment (DHA numbering), was converted to the C17-C22 phosphonium salt, which was subjected to a Wittig reaction with racemic C16-aldehyde of the C12-C16 part with the TMS and TBS-oxy groups at C12 and C14, yielding the C12-C22 derivative with 14R/S and 21R chirality. Kinetic resolution using Sharpless asymmetric epoxidation of the TBS-deprotected allylic alcohol with l-(+)-DIPT/Ti(O-i-Pr) 4 afforded 14S-epoxy alcohol and 14R-allylic alcohol with >99% diastereomeric excess (de) for both. The CN group was introduced to the epoxy alcohol by reaction with Et 2 AlCN. The 14R-allylic alcohol was also converted to the nitrile via Mitsunobu inversion. Reduction of the nitrile with DIBAL afforded the key aldehyde corresponding to the C11-C22 moiety. The Wittig reaction of this aldehyde with a phosphonium salt of the remaining C1-C10 part followed by functional group manipulation gave 14S,21R-diHDHA. Similarly, ethyl (S)-lactate (>99% ee) was converted to 14S,21S-diHDHA. The chiral LC-UV-MS/MS analysis demonstrated that each of these two 14,21-diHDHAs synthesized using the presented total organic synthesis was highly stereoselective and identical to the macrophage-produced counterpart.

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Alveolar macrophages drive hepatocellular carcinoma lung metastasis by generating leukotriene B4.

Nosaka T, *Baba T, Tanabe Y, Sasaki S, Nishimura T, Imamura Y, Yurino H, Hashimoto S, Arita M, Nakamoto Y, Mukaida Y.

J Immunol (Journal of Immunology)  200 ( 5 ) 1839 - 1852 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  00221767

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© 2018 by The American Association of Immunologists, Inc. All rights reserved. Macrophages in lungs can be classified into two subpopulations, alveolar macrophages (AMs) and interstitial macrophages (IMs), which reside in the alveolar and interstitial spaces, respectively. Accumulating evidence indicates the involvement of IMs in lung metastasis, but the roles of AMs in lung metastasis still remain elusive. An i.v. injection of a mouse hepatocellular carcinoma (HCC) cell line, BNL, caused lung metastasis foci with infiltration of AMs and IMs. Comprehensive determination of arachidonic acid metabolite levels revealed increases in leukotrienes and PGs in lungs in this metastasis model. A 5-lipoxygenase (LOX) inhibitor but not a cyclooxygenase inhibitor reduced the numbers of metastatic foci, particularly those of a larger size. A major 5-LOX metabolite, LTB 4 , augmented in vitro cell proliferation of human HCC cell lines as well as BNL cells. Moreover, in this lung metastasis course, AMs exhibited higher expression levels of the 5-LOX and LTB 4 than IMs. Consistently, 5-LOX-expressing AMs increased in the lungs of human HCC patients with lung metastasis, compared with those without lung metastasis. Furthermore, intratracheal clodronate liposome injection selectively depleted AMs but not IMs, together with reduced LTB 4 content and metastatic foci numbers in this lung metastasis process. Finally, IMs in mouse metastatic foci produced CCL2, thereby recruiting blood-borne, CCR2-expressing AMs into lungs. Thus, AMs can be recruited under the guidance of IM-derived CCL2 into metastatic lungs and can eventually contribute to the progression of lung metastasis by providing a potent arachidonic acid-derived tumor growth promoting mediator, LTB 4 .

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Reduction of lipid accumulation rescues Bietti’s crystalline dystrophy phenotypes.

Hata M, *Ikeda H, Iwai S, Iida Y, Gotoh N, Asaka I, Ikeda K, Isobe Y, Hori A, Nakagawa S, Yamato S, Arita M, Yoshimura N, Tsujikawa A.

Proc Natl Acad Sci USA (Proceedings of the National Academy of Sciences of the United States of America)  115 ( 15 ) 3936 - 3941 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  00278424

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© 2018 National Academy of Sciences. All Rights Reserved. Bietti's crystalline dystrophy (BCD) is an intractable and progressive chorioretinal degenerative disease caused by mutations in the CYP4V2 gene, resulting in blindness in most patients. Although we and others have shown that retinal pigment epithelium (RPE) cells are primarily impaired in patients with BCD, the underlying mechanisms of RPE cell damage are still unclear because we lack access to appropriate disease models and to lesion-affected cells from patients with BCD. Here, we generated human RPE cells from induced pluripotent stem cells (iPSCs) derived from patients with BCD carrying a CYP4V2 mutation and successfully established an in vitro model of BCD, i.e., BCD patient-specific iPSC-RPE cells. In this model, RPE cells showed degenerative changes of vacuolated cytoplasm similar to those in postmortem specimens from patients with BCD. BCD iPSC-RPE cells exhibited lysosomal dysfunction and impairment of autophagy flux, followed by cell death. Lipidomic analyses revealed the accumulation of glucosylceramide and free cholesterol in BCD-affected cells. Notably, we found that reducing free cholesterol by cyclodextrins or δ-tocopherol in RPE cells rescued BCD phenotypes, whereas glucosylceramide reduction did not affect the BCD phenotype. Our data provide evidence that reducing intracellular free cholesterol may have therapeutic efficacy in patients with BCD.

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Identification of protein targets of 12/15-lipoxygenase-derived lipid electrophiles in mouse peritoneal macrophages using omega-alkynyl fatty acid.

Isobe Y, Kawashima Y, Ishihara T, Watanabe K, Ohara O, *Arita M.

ACS Chem Biol (ACS Chemical Biology)  13 ( 4 ) 887 - 893 2018

Research paper (scientific journal), Joint Work, Accepted,  ISSN  15548929

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© 2018 American Chemical Society. The 12/15-lipoxygenase (12/15-LOX) enzyme introduces peroxyl groups, in a position-specific manner, into polyunsaturated fatty acids to form various kinds of bioactive lipid metabolites, including lipid-derived electrophiles (LDE). The resident peritoneal macrophage is the site of highest 12/15-LOX expression in the mouse. However, the role of the enzyme in the regulation of resident macrophages is not fully understood. Here, we describe a chemoproteomic method to identify the targets of enzymatically generated LDE. By treating mouse peritoneal macrophages with omega-alkynyl arachidonic acid (aAA), we identified a series of proteins adducted by LDE generated through a 12/15-LOX catalyzed reaction. Pathway analysis revealed a dramatic enrichment of proteins involved in energy metabolism and found that glycolytic flux and mitochondrial respiration were significantly affected by the expression of 12/15-LOX. Our findings thus highlight the utility of chemoproteomics using aAA for identifying intracellular targets of enzymatically generated LDE.

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Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid.

Isobe Y, Itagaki M, Ito Y, Naoe S, Kojima K, Ikeguchi M, *Arita M

Sci Rep (Scientific Reports)  8 ( 1 ) 7954 2018

Research paper (scientific journal), Joint Work, Accepted

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© 2018 The Author(s). Metabolites generated via oxygenation of the omega-3 double bond (omega-3 oxygenation) in eicosapentaenoic acid (EPA) have recently been identified as novel anti-inflammatory lipid mediators. Therefore, oxygenase(s) responsible for this metabolic pathway are of particular interest. We performed genome-wide screening of mouse cytochrome P450 (CYP) isoforms to explore enzymes involved in omega-3 oxygenation of EPA. As a result, 5 CYP isoforms (mouse Cyp1a2, 2c50, 4a12a, 4a12b, and 4f18) were selected and identified to confer omega-3 epoxidation of EPA to yield 17,18-epoxyeicosatetraenoic acid (17,18-EpETE). Stereoselective production of 17,18-EpETE by each CYP isoform was confirmed, and molecular modeling indicated that chiral differences stem from different EPA binding conformations in the catalytic domains of respective CYP enzymes.

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