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Article ; Online: The role of dendritic cells and their immunometabolism in rheumatoid arthritis.

Suwa, Yuichi / Nagafuchi, Yasuo / Yamada, Saeko / Fujio, Keishi

2023 Volume 14, Page(s) 1161148

Abstract: Dendritic cells (DCs) play crucial roles in the pathogenesis of rheumatoid arthritis (RA), a prototypic autoimmune disease characterized by chronic synovitis and joint destruction. Conventional dendritic cells (cDCs) with professional antigen-presenting ... ...

Abstract	Dendritic cells (DCs) play crucial roles in the pathogenesis of rheumatoid arthritis (RA), a prototypic autoimmune disease characterized by chronic synovitis and joint destruction. Conventional dendritic cells (cDCs) with professional antigen-presenting functions are enriched in the RA synovium. In the synovium, the cDCs are activated and show both enhanced migratory capacities and T cell activation in comparison with peripheral blood cDCs. Plasmacytoid dendritic cells, another subtype of DCs capable of type I interferon production, are likely to be tolerogenic in RA. Monocyte-derived dendritic cells (moDCs), once called "inflammatory DCs", are localized in the RA synovium, and they induce T-helper 17 cell expansion and enhanced proinflammatory cytokine production. Recent studies revealed that synovial proinflammatory hypoxic environments are linked to metabolic reprogramming. Activation of cDCs in the RA synovium is accompanied by enhanced glycolysis and anabolism. In sharp contrast, promoting catabolism can induce tolerogenic DCs from monocytes. Herein, we review recent studies that address the roles of DCs and their immunometabolic features in RA. Immunometabolism of DCs could be a potential therapeutic target in RA.
MeSH term(s)	Humans ; Arthritis, Rheumatoid ; Synovial Membrane ; Autoimmune Diseases/metabolism ; Monocytes/metabolism ; Dendritic Cells
Language	English
Publishing date	2023-05-12
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1161148
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Article ; Online: Pulmonary Hypertension Associated with Anti-synthetase Syndrome: A Case Report and Literature Review.

Yoshitomi, Yutaro / Suwa, Yuichi / Tsuchiya, Haruka / Goto, Manaka / Natsumoto, Bunki / Shoda, Hirofumi / Fujio, Keishi

Internal medicine (Tokyo, Japan)

2023 Volume 62, Issue 24, Page(s) 3685–3689

Abstract: Pulmonary hypertension (PH) is a serious condition in which there is an abnormally high pressure in the pulmonary arteries that can occur as a complication of connective tissue diseases. Although the relationship between PH and systemic lupus ... ...

Abstract	Pulmonary hypertension (PH) is a serious condition in which there is an abnormally high pressure in the pulmonary arteries that can occur as a complication of connective tissue diseases. Although the relationship between PH and systemic lupus erythematosus or systemic sclerosis has been well-characterized, PH rarely occurs in patients with anti-synthetase syndrome (ASS), and little is known about the pathophysiology and clinical outcome of patients with ASS-PH. We herein report a patient with anti-Jo-1-positive ASS complicated by PH and discuss the treatment strategy through a review of previously reported cases.
MeSH term(s)	Humans ; Hypertension, Pulmonary/complications ; Hypertension, Pulmonary/drug therapy ; Connective Tissue Diseases/complications ; Scleroderma, Systemic/complications ; Lupus Erythematosus, Systemic/complications ; Pulmonary Artery
Language	English
Publishing date	2023-04-14
Publishing country	Japan
Document type	Review ; Case Reports ; Journal Article
ZDB-ID	32371-8
ISSN	1349-7235 ; 0021-5120 ; 0918-2918
ISSN (online)	1349-7235
ISSN	0021-5120 ; 0918-2918
DOI	10.2169/internalmedicine.9809-22
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Article: Measurement of the potential rates of dissimilatory nitrate reduction to ammonium based on 14nh4+/15nh4+ analyses via sequential conversion to n2o

Kuroiwa, Megumi / Fukushima, Keitaro / Hashimoto, Kazuma / Senga, Yukiko / Sato, Tsubasa / Katsuyama, Chie / Suwa, Yuichi

Journal of visualized experiments. 2020 Oct. 07, , no. 164

2020

Abstract: The importance of understanding the fate of nitrate (NO3−), which is the dominant N species transferred from terrestrial to aquatic ecosystems, has been increasing because global nitrogen loads have dramatically increased following industrialization. ... ...

Abstract	The importance of understanding the fate of nitrate (NO3−), which is the dominant N species transferred from terrestrial to aquatic ecosystems, has been increasing because global nitrogen loads have dramatically increased following industrialization. Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are both microbial processes that use NO3− for respiration. Compared to denitrification, quantitative determinations of the DNRA activity have been carried out only to a limited extent. This has led to an insufficient understanding of the importance of DNRA in NO3− transformations and the regulating factors of this process. The objective of this paper is to provide a detailed procedure for the measurement of the potential DNRA rate in environmental samples. In brief, the potential DNRA rate can be calculated from the 15N-labeled ammonium (15NH4+) accumulation rate in 15NO3− added incubation. The determination of the 14NH4+ and 15NH4+ concentrations described in this paper is comprised of the following steps. First, the NH4+ in the sample is extracted and trapped on an acidified glass filter as ammonium salt. Second, the trapped ammonium is eluted and oxidized to NO3− via persulfate oxidation. Third, the NO3− is converted to N2O via an N2O reductase deficient denitrifier. Finally, the converted N2O is analyzed using a previously developed quadrupole gas chromatography–mass spectrometry system. We applied this method to salt marsh sediments and calculated their potential DNRA rates, demonstrating that the proposed procedures allow a simple and more rapid determination compared to previously described methods.
Keywords	ammonium ; ammonium salts ; denitrification ; denitrifying microorganisms ; gas chromatography-mass spectrometry ; glass ; industrialization ; nitrate reduction ; nitrates ; nitrogen ; nitrous-oxide reductase ; oxidation ; salt marshes
Language	English
Dates of publication	2020-1007
Size	p. e59562.
Publishing place	Journal of Visualized Experiments
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/59562
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Article ; Online: Measurement of the Potential Rates of Dissimilatory Nitrate Reduction to Ammonium Based on 14NH4 +/15NH4 + Analyses via Sequential Conversion to N2O.

Kuroiwa, Megumi / Fukushima, Keitaro / Hashimoto, Kazuma / Senga, Yukiko / Sato, Tsubasa / Katsuyama, Chie / Suwa, Yuichi

Journal of visualized experiments : JoVE

2020 , Issue 164

Abstract: The importance of understanding the fate of nitrate ( ... ...

Abstract	The importance of understanding the fate of nitrate (NO3
MeSH term(s)	Ammonium Compounds/metabolism ; Calibration ; Geologic Sediments/chemistry ; Nitrates/metabolism ; Nitrites/isolation & purification ; Nitrogen Isotopes/metabolism ; Nitrous Oxide/metabolism ; Oxidation-Reduction ; Oxygen/isolation & purification ; Polytetrafluoroethylene ; Pseudomonas/metabolism ; Time Factors
Chemical Substances	Ammonium Compounds ; Nitrates ; Nitrites ; Nitrogen Isotopes ; Polytetrafluoroethylene (9002-84-0) ; Nitrous Oxide (K50XQU1029) ; Oxygen (S88TT14065)
Language	English
Publishing date	2020-10-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/59562
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Article: Anammox and Denitrification in the Intertidal Sediment of the Hypereutrophic Yatsu Tidal Flat, Japan

Senga, Yukiko / Kuroiwa, Megumi / Nohara, Seiichi / Sato, Tsubasa / Suwa, Yuichi

Estuaries and coasts. 2019 May, v. 42, no. 3

2019

Abstract: An increase in available nitrogen loading in intertidal ecosystems causes eutrophication and macroalgae blooms. Denitrification and anaerobic ammonium oxidation (anammox) lead to the removal of bioavailable nitrogen, but few studies have examined this in ...

Abstract	An increase in available nitrogen loading in intertidal ecosystems causes eutrophication and macroalgae blooms. Denitrification and anaerobic ammonium oxidation (anammox) lead to the removal of bioavailable nitrogen, but few studies have examined this in intertidal sediments. The sediment anammox and denitrification rates in September 2015 and November 2016 were measured using a 15N tracer technique at two sites, with and without macroalgae, in the hypereutrophic Yatsu tidal flat, eastern Japan. At both sites, the rate of N2 production via anammox was consistently low compared with that via denitrification, accounting for < 7% of the total N2 production. In a fed-batch incubation experiment, the anammox rate increased in the surface sediment after 3 months. However, the contribution of anammox to nitrogen removal did not exceed that of denitrification, suggesting that denitrification is the major pathway for conversion of inorganic nitrogen to N2, and that anammox plays a limited role in nitrogen removal in the Yatsu tidal flat. Denitrification activity measured from August 2012 to January 2017 using the acetylene block method was higher in the sediment with macroalgae than that without. Multiple linear regression analysis revealed that denitrification in the sediment with macroalgae was limited by the nitrogen substrate, likely due to competition with macroalgae for nitrogen. Temperature and H2S production under macroalgae cover might also affect denitrification. In comparison, the organic carbon content was a key factor regulating heterotrophic denitrification in the sediment without macroalgae. These findings suggest that the occurrence of macroalgae changes the progress of denitrification in intertidal ecosystems.
Keywords	acetylene ; anaerobic ammonium oxidation ; bioavailability ; denitrification ; ecosystems ; eutrophication ; hydrogen sulfide ; littoral zone ; macroalgae ; nitrogen ; organic carbon ; pollution load ; regression analysis ; sediments ; stable isotopes ; temperature ; tracer techniques ; Japan
Language	English
Dates of publication	2019-05
Size	p. 665-674.
Publishing place	Springer US
Document type	Article
ZDB-ID	2229170-2
ISSN	1559-2731 ; 1559-2723
ISSN (online)	1559-2731
ISSN	1559-2723
DOI	10.1007/s12237-019-00520-6
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Article ; Online: The physiological potential of anammox bacteria as revealed by their core genome structure.

Okubo, Takashi / Toyoda, Atsushi / Fukuhara, Kohei / Uchiyama, Ikuo / Harigaya, Yuhki / Kuroiwa, Megumi / Suzuki, Takuma / Murakami, Yuka / Suwa, Yuichi / Takami, Hideto

DNA research : an international journal for rapid publication of reports on genes and genomes

2020 Volume 28, Issue 1

Abstract: We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) ... ...

Abstract	We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2- reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.
MeSH term(s)	Ammonium Compounds/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Bacteria, Anaerobic/genetics ; Bacteria, Anaerobic/metabolism ; Bacteria, Anaerobic/physiology ; Genome, Bacterial ; Metagenome ; Nitrite Reductases ; Oxidoreductases ; Sequence Analysis, DNA
Chemical Substances	Ammonium Compounds ; Oxidoreductases (EC 1.-) ; Nitrite Reductases (EC 1.7.-) ; hydroxylamine dehydrogenase (EC 1.7.2.6)
Language	English
Publishing date	2020-12-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1212508-8
ISSN	1756-1663 ; 1340-2838
ISSN (online)	1756-1663
ISSN	1340-2838
DOI	10.1093/dnares/dsaa028
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Article ; Online: Deteriorating anemia in an 86-year-old man was improved by prednisolone.

Kitago, Moe / Kase, Yoshitaka / Iwata, Yuko / Suwa, Yuichi / Tsuchiya, Haruka / Hanata, Norio / Kojima, Taro / Ogawa, Sumito / Fujio, Keishi / Akishita, Masahiro

Geriatrics & gerontology international

2020 Volume 20, Issue 11, Page(s) 1091–1092

MeSH term(s)	Aged, 80 and over ; Anemia/drug therapy ; Anti-Inflammatory Agents/therapeutic use ; Humans ; Japan ; Male ; Microscopic Polyangiitis/diagnosis ; Prednisolone/therapeutic use
Chemical Substances	Anti-Inflammatory Agents ; Prednisolone (9PHQ9Y1OLM)
Language	English
Publishing date	2020-09-20
Publishing country	Japan
Document type	Case Reports ; Letter
ZDB-ID	2113849-7
ISSN	1447-0594 ; 1444-1586
ISSN (online)	1447-0594
ISSN	1444-1586
DOI	10.1111/ggi.14024
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Article: Uncoupling of ammonia oxidation from nitrite oxidation: Impact upon nitrous oxide production in non-cropped Oregon soils

Giguere, Andrew T / Bottomley, Peter J / Myrold, David D / Suwa, Yuichi / Taylor, Anne E

Soil biology & biochemistry. 2017 Jan., v. 104

2017

Abstract: The factors controlling the relative contributions of ammonia- (NH3) oxidizing archaea (AOA) and bacteria (AOB) to nitrification and nitrous oxide (N2O) production in soil remain unclear. A study was conducted to examine the contributions of AOA and AOB ... ...

Abstract	The factors controlling the relative contributions of ammonia- (NH3) oxidizing archaea (AOA) and bacteria (AOB) to nitrification and nitrous oxide (N2O) production in soil remain unclear. A study was conducted to examine the contributions of AOA and AOB to nitrification, nitrite (NO2−) accumulation, and NO2−-affected N2O production in three non-cropped Oregon soils. Nitrification potential rates in the three soils ranged seven-fold from 0.15 to 1.08 μmol N g−1 d−1, with AOA contributing 64–71% of the total activity. AOA- and AOB-driven NO2− accumulation represented 8–100% of total NO2− + NO3− accumulation, persisted over 48 h, and was accompanied by acetylene-sensitive, ammonium- (NH4+) stimulated N2O production. Ammonium- and NO2−-dependent N2O production occurred when both AOA and AOB, or AOA alone were active. By adding the NO2−-oxidizing bacteria, Nitrobacter vulgaris, to soil slurries to increase NO2−-oxidizing capacity, both NO2− accumulation and N2O production were prevented, while the overall rate of nitrification was unaffected. Yields of N2O-N amounted to 0.05 ± 0.01% of total NO2− + NO3−-N accumulation in the presence of supplemental NH4+, and 0.28 ± 0.11% in the presence of both supplemental NH4+ + NO2−. Regression analysis of the N2O production against NO2− accumulation over 24 h revealed a positive, non-linear relationship for N2O production by both AOA plus AOB and by AOA alone. Values of Vmax ranged 12-fold from 0.05 to 0.62 nmol N2O g−1 d−1, and predicted Km values for NO2− ranged 15-fold from 0.02 to 0.30 μmol NO2− g−1 soil. These findings provide new insights into the impact of NO2− accumulation in soils on N2O production by both AOA and AOB, and show that NO2− accumulation primarily drives N2O formation in these soils, and increases N2O yield by both AOA and AOB.
Keywords	ammonia ; ammonium compounds ; bacteria ; nitrates ; nitrification ; nitrites ; Nitrobacter vulgaris ; nitrogen dioxide ; nitrous oxide ; oxidation ; regression analysis ; slurries ; soil ; Oregon
Language	English
Dates of publication	2017-01
Size	p. 30-38.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2016.10.011
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Article ; Online: Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance.

Yamada, Saeko / Nagafuchi, Yasuo / Wang, Min / Ota, Mineto / Hatano, Hiroaki / Takeshima, Yusuke / Okubo, Mai / Kobayashi, Satomi / Sugimori, Yusuke / Masahiro, Nakano / Yoshida, Ryochi / Hanata, Norio / Suwa, Yuichi / Tsuchida, Yumi / Iwasaki, Yukiko / Sumitomo, Shuji / Kubo, Kanae / Shimane, Kenichi / Setoguchi, Keigo /

Azuma, Takanori / Kanda, Hiroko / Shoda, Hirofumi / Zhang, Xuan / Yamamoto, Kazuhiko / Ishigaki, Kazuyoshi / Okamura, Tomohisa / Fujio, Keishi

Annals of the rheumatic diseases

2023 Volume 82, Issue 6, Page(s) 809–819

Abstract: Objectives: Little is known about the immunology underlying variable treatment response in rheumatoid arthritis (RA). We performed large-scale transcriptome analyses of peripheral blood immune cell subsets to identify immune cells that predict treatment ...

Abstract	Objectives: Little is known about the immunology underlying variable treatment response in rheumatoid arthritis (RA). We performed large-scale transcriptome analyses of peripheral blood immune cell subsets to identify immune cells that predict treatment resistance. Methods: We isolated 18 peripheral blood immune cell subsets of 55 patients with RA requiring addition of new treatment and 39 healthy controls, and performed RNA sequencing. Transcriptome changes in RA and treatment effects were systematically characterised. Association between immune cell gene modules and treatment resistance was evaluated. We validated predictive value of identified parameters for treatment resistance using quantitative PCR (qPCR) and mass cytometric analysis cohorts. We also characterised the identified population by synovial single cell RNA-sequencing analysis. Results: Immune cells of patients with RA were characterised by enhanced interferon and IL6-JAK-STAT3 signalling that demonstrate partial normalisation after treatment. A gene expression module of plasmacytoid dendritic cells (pDC) reflecting the expansion of dendritic cell precursors (pre-DC) exhibited strongest association with treatment resistance. Type I interferon signalling was negatively correlated to pre-DC gene expression. qPCR and mass cytometric analysis in independent cohorts validated that the pre-DC associated gene expression and the proportion of pre-DC were significantly higher before treatment in treatment-resistant patients. A cluster of synovial DCs showed both features of pre-DC and pro-inflammatory conventional DC2s. Conclusions: An increase in pre-DC in peripheral blood predicted RA treatment resistance. Pre-DC could have pathophysiological relevance to RA treatment response.
MeSH term(s)	Humans ; Arthritis, Rheumatoid/drug therapy ; Arthritis, Rheumatoid/genetics ; Transcriptome ; Gene Expression Profiling ; Dendritic Cells
Language	English
Publishing date	2023-03-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	7090-7
ISSN	1468-2060 ; 0003-4967
ISSN (online)	1468-2060
ISSN	0003-4967
DOI	10.1136/ard-2022-223645
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Article ; Online: Quantitative evaluation of inhibitory effect of various substances on anaerobic ammonia oxidation (anammox).

Nakamura, Tomotaka / Harigaya, Yuhki / Kimura, Yuya / Kuroiwa, Megumi / Kurata, Yuhri / Isaka, Kazuichi / Suwa, Yuichi

Journal of bioscience and bioengineering

2017 Volume 124, Issue 3, Page(s) 333–338

Abstract: The inhibitory effect of 20 substances of various chemical species on the anaerobic ammonia oxidation (anammox) activity of an enrichment culture, predominated by Candidatus Brocadia, was determined systematically by using ... ...

Abstract	The inhibitory effect of 20 substances of various chemical species on the anaerobic ammonia oxidation (anammox) activity of an enrichment culture, predominated by Candidatus Brocadia, was determined systematically by using a
Language	English
Publishing date	2017-09
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1465387-4
ISSN	1347-4421 ; 1389-1723
ISSN (online)	1347-4421
ISSN	1389-1723
DOI	10.1016/j.jbiosc.2017.04.010
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