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Tomomi Ichinose Last modified date:2020.12.27

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Academic Degree
Country of degree conferring institution (Overseas)
Field of Specialization
Plant physiology
Total Priod of education and research career in the foreign country
Academic Activities
1. Kataoka Y, Iimori M, Fujisawa R, Morikawa-Ichinose T, Niimi S, Wakasa T, Saeki H, Oki E, Miura D, Tsurimoto T, Maehara Y, Kitao H., DNA replication stress induced by trifluridine determines tumor cell fate according to p53 status., Mol Cancer Res., DOI: 10.1158/1541-7786., 2020.09, DNA replication stress (DRS) is a predominant cause of genome instability, a driver of tumorigenesis and malignant progression. Nucleoside analogue-type chemotherapeutic drugs introduce DNA damage and exacerbate DRS in tumor cells. However, the mechanisms underlying the antitumor effect of these drugs are not fully understood. Here, we show that the fluorinated thymidine analogue trifluridine (FTD), an active component of the chemotherapeutic drug trifluridine/tipiracil, delayed DNA synthesis by human replicative DNA polymerases by acting both as an inefficient deoxyribonucleotide triphosphate source (FTD triphosphate) and as an obstacle base (trifluorothy- mine) in the template DNA strand, which caused DRS. In cells, FTD decreased the thymidine triphosphate level in the dNTP pool and increased the FTD triphosphate level, resulting in the activation of DRS-induced cellular responses during S-phase. In addition, replication protein A–coated single-stranded DNA associated with FancD2 and accumulated after tumor cells completed S-phase. Finally, FTD activated the p53–p21 pathway and suppressed tumor cell growth by inducing cellular senes- cence via mitosis skipping. In contrast, tumor cells that lost wild- type p53 underwent apoptotic cell death via aberrant late mitosis with severely impaired separation of sister chromatids. These results demonstrate that DRS induced by a nucleoside analogue– type chemotherapeutic drug suppresses tumor growth irrespec- tive of p53 status by directing tumor cell fate toward cellular senescence or apoptotic cell death according to p53 status..
2. Morikawa-Ichinose T, Miura D, Zhang L, Kim SJ, Maruyama-Nakashita A., Involvement of BGLU30 in glucosinolate catabolism in the Arabidopsis leaf under dark conditions., Plant Cell Physiol.,, 61, 6, 1095-1106, 2020.04, Glucosinolates (GSLs) are secondary metabolites that play important roles in plant defense and are suggested to act as storage compounds. Despite their important roles, metabolic dynamics of GSLs under various growth conditions remain poorly understood. To determine how light conditions influence the levels of different GSLs and their distribution in Arabidopsis leaves, we visualized the GSLs under different light conditions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We observed the unique distribution patterns of each GSL in the inner regions of leaves and marked decreases under darkness, indicating light conditions influenced GSL metabolism. GSLs are hydrolyzed by a group of ß-glucosidase (BGLU) called myrosinase. Previous transcriptome data for GSL metabolism under light and dark conditions have revealed the highly induced expression of BGLU30, one of the putative myrosinases, which is also annotated as Dark INducible2, under darkness. Impairment of the darkness-induced GSL decrease in the disruption mutants of BGLU30, bglu30, indicated that BGLU30 mediated GSL hydrolysis under darkness. Based on the GSL profiles in the wild-type and bglu30 leaves under both conditions, short-chain GSLs were potentially preferable substrates for BGLU30. Our findings provide an effective way of visualizing GSL distribution in plants and highlighted the carbon storage GSL function..
3. Zhang L, Kawaguchi R, Morikawa-Ichinose T, Allahham A, Kim SJ, Maruyama-Nakashita A., Sulfur deficiency-induced glucosinolate catabolism attributed to two beta-glucosidases, BGLU28 and BGLU30, is required for plant growth maintenance under sulfur deficiency., Plant Cell Physiol, doi: 10.1093/pcp/pcaa006., 61, 4, 803-813, 2020.02, Sulfur (S) is an essential element for plants, and S deficiency causes severe growth retardation. Although the catabolic process of glucosinolates (GSLs), the major S-containing metabolites specific to Brassicales including Arabidopsis, has been recognized as one of the S deficiency (-S) responses in plants, the physiological function of this metabolic process is not clear. Two β-glucosidases (BGLUs), BGLU28 and BGLU30, are assumed to be responsible for this catabolic process as their transcript levels were highly upregulated by -S. To clarify the physiological function of BGLU28 and BGLU30 and their roles in GSL catabolism, we analyzed the accumulation of GSLs and other S-containing compounds in the single and double mutant lines of BGLU28 and BGLU30 and in wild-type plants under different S conditions. GSL levels were highly increased, while the levels of sulfate, cysteine, glutathione and protein were decreased in the double mutant line of BGLU28 and BGLU30 (bglu28/30) under -S. Furthermore, transcript level of Sulfate Transporter1;2, the main contributor of sulfate uptake from the environment, was increased in bglu28/30 mutants under -S. With these metabolic and transcriptional changes, bglu28/30 mutants displayed obvious growth retardation under -S. Overall, our results indicate that BGLU28 and BGLU30 are required for -S-induced GSL catabolism and contribute to sustained plant growth under -S by recycling sulfate to primary S metabolism..
4. Morikawa-Ichinose T, Fujimura Y, Murayama F, Yamazaki Y, Yamamoto T, Wariishi H, Miura D., Improvement of sensitivity and reproducibility for imaging of endogenous metabolites by matrix-assisted laser desorption/ionization-mass spectrometry., J Am Soc Mass Spectrom., doi: 10.1007/s13361-019-02221-7., 30, 8, 1512-1520, 2019.04, Matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) is a powerful technique to visualize the distributions of biomolecules without any labeling. In MALDI-MSI experiments, the choice of matrix deposition method is important for acquiring favorable MSI data with high sensitivity and high reproducibility. Generally, manual or automated spray-coating and automated sublimation methods are used, but these methods have some drawbacks with respect to detection sensitivity, spatial resolution, and data reproducibility. Herein, we present an optimized matrix deposition method of sublimation coupled with recrystallization using 9-aminoacridine (9-AA) as a matrix capable of ionizing endogenous metabolites. The matrix recrystallization process after sublimation was optimized for the solvent concentration and reaction temperature for matrix-metabolite co-crystallization. This optimized method showed excellent reproducibility and spatial resolution compared to the automatic spray-coating method. Furthermore, the recrystallization step after sublimation remarkably improved the detectability of metabolites, including amino acids, nucleotide derivatives, and lipids, compared with the conventional sublimation method. To date, there have been no other reports of 9-AA-based sublimation combined with recrystallization. The present method provides an easy, sensitive, and reproducible matrix deposition method for MALDI-MSI of endogenous metabolites..
5. Morikawa-Ichinose T, Kim SJ, Allahham A, Kawaguchi R, Maruyama-Nakashita A., Glucosinolate distribution in the aerial parts of sel1-10, a disruption mutant of the sulfate transporter SULTR1;2, in mature Arabidopsis thaliana plants., Plants., doi: 10.3390/plants8040095., 8, 4, 95, 2019.04, Plants take up sulfur (S), an essential element for all organisms, as sulfate, which is mainly attributed to the function of SULTR1;2 in Arabidopsis. A disruption mutant of SULTR1;2, sel1-10, has been characterized with phenotypes similar to plants grown under sulfur deficiency (-S). Although the effects of -S on S metabolism were well investigated in seedlings, no studies have been performed on mature Arabidopsis plants. To study further the effects of -S on S metabolism, we analyzed the accumulation and distribution of S-containing compounds in different parts of mature sel1-10 and of the wild-type (WT) plants grown under long-day conditions. While the levels of sulfate, cysteine, and glutathione were almost similar between sel1-10 and WT, levels of glucosinolates (GSLs) differed between them depending on the parts of the plant. GSLs levels in the leaves and stems were generally lower in sel1-10 than those in WT. However, sel1-10 seeds maintained similar levels of aliphatic GSLs to those in WT plants. GSL accumulation in reproductive tissues is likely to be prioritized even when sulfate supply is limited in sel1-10 for its role in S storage and plant defense..
6. Edahiro K, Iimori M, Kobunai T, Morikawa-Ichinose T, Miura D, Kataoka Y, Niimi S, Wakasa T, Saeki H, Oki E, Kitao H, Maehara Y, Thymidine kinase 1 loss confers trifluridine resistance without affecting 5-fluorouracil metabolism and cytotoxicity., Mol Cancer Res., DOI: 10.1158/1541-7786., 16, 10, 1483-1490, 2018.06, Acquired resistance to therapeutic drugs is a serious problem for patients with cancer receiving systemic treatment. Experimentally, drug resistance is established in cell lines in vitro by repeated, continuous exposure to escalating concentrations of the drug; however, the precise mechanism underlying the acquired resistance is not always known. Here, it is demonstrated that the human colorectal cancer cell line DLD1 with acquired resistance to trifluridine (FTD), a key component of the novel, orally administered nucleoside analogue-type chemotherapeutic drug trifluridine/tipiracil, lacks functional thymidine kinase 1 (TK1) expression because of one nonsense mutation in the coding exon. Targeted disruption of the TK1 gene also conferred severe FTD resistance, indicating that the loss of TK1 protein expression is the primary cause of FTD resistance. Both FTD-resistant DLD1 cells and DLD1-TK1 -/- cells exhibited similar 5-fluorouracil (5-FU) sensitivity to that of the parental DLD1 line. The quantity of cellular pyrimidine nucleotides in these cells and the kinetics of thymidylate synthase ternary complex formation in 5-FU-treated cells is similar to DLD1 cells, indicating that 5-FU metabolism and cytotoxicity were unaffected. The current data provide molecular-based evidence that acquired resistance to FTD does not confer 5-FU resistance, implying that 5-FU-based chemotherapy would be effective even in tumors that become refractory to FTD during trifluridine/tipiracil treatment..
7. Sato E, Saigusa D, Mishima E, Uchida T, Miura D, Morikawa-Ichinose T, Kisu K, Sekimoto A, Saito R, Oe Y, Matsumoto Y, Tomioka Y, Mori T, Takahashi N, Sato H, Abe T, Niwa T, Ito S., Impact of the oral adsorbent AST-120 on organ-specific accumulation of uremic toxins: LC-MS/MS and MS imaging techniques., Toxins, doi:10.3390/toxins10010019, 10, 19, 1-15, 2018.01, Elevated circulating uremic toxins are associated with a variety of symptoms and organ dysfunction observed in patients with chronic kidney disease (CKD). Indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are representative uremic toxins that exert various harmful effects. We recently showed that IS induces metabolic alteration in skeletal muscle and causes sarcopenia in mice. However, whether organ-specific accumulation of IS and PCS is associated with tissue dysfunction is still unclear. We investigated the accumulation of IS and PCS using liquid chromatography/tandem mass spectrometry in various tissues from mice with adenine-induced CKD. IS and PCS accumulated in all 15 organs analyzed, including kidney, skeletal muscle, and brain. We also visualized the tissue accumulation of IS and PCS with immunohistochemistry and mass spectrometry imaging techniques. The oral adsorbent AST-120 prevented some tissue accumulation of IS and PCS. In skeletal muscle, reduced accumulation following AST-120 treatment resulted in the amelioration of renal failure-associated muscle atrophy. We conclude that uremic toxins can accumulate in various organs and that AST-120 may be useful in treating or preventing organ dysfunction in CKD, possibly by reducing tissue accumulation of uremic toxins..
8. Nakamura J, Morikawa-Ichinose T, Fujimura Y, Hayakawa E, Takahashi K, Ishii T, Miura D, and Wariishi H, Spatially resolved metabolic distribution for unraveling the physiological change and responses in tomato fruit using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI)., Anal Bioanal Chem., DOI 10.1007/s00216-016-0118-4, 409, 1697-1706, 2017.01, Information on spatiotemporal metabolic behavior is indispensable for a precise understanding of physiological changes and responses, including those of ripening processes and wounding stress, in fruit, but such information is still limited. Here, we visualized the spatial distribution of metabolites within tissue sections of tomato (Solanum lycopersicum L.) fruit using a matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI–MSI) technique combined with a matrix sublimation/recrystallization method. This technique elucidated the unique distribution patterns of more than 30 metabolite-derived ions, including primary and secondary metabolites, simultaneously. To investigate spatiotemporal metabolic alterations during physiological changes at the whole-tissue level, MALDI–MSI was performed using the different ripening phenotypes of mature green and mature red tomato fruits. Although apparent alterations in the localization and intensity of many detected metabolites were not observed between the two tomatoes, the amounts of glutamate and adenosine monophosphate, umami compounds, increased in both mesocarp and locule regions during the ripening process. In contrast, malate, a sour compound, decreased in both regions. MALDI–MSI was also applied to evaluate more local metabolic responses to wounding stress. Accumulations of a glycoalkaloid, tomatine, and a low level of its glycosylated metabolite, esculeoside A, were found in the wound region where cell death had been induced. Their inverse levels were observed in non-wounded regions. Furthermore, the amounts of both compounds differed in the developmental stages. Thus, our MALDI–MSI technique increased the understanding of the physiological changes and responses of tomato fruit through the determination of spatiotemporally resolved metabolic alterations..
9. Sato E, Mori T, Mishima E, Suzuki A, Sugawara S, Kurasawa N, Saigusa D, Miura D, Morikawa-Ichinose T, Saito R, Oba-Yabana I, Oe Y, Kisu K, Naganuma E, Koizumi K, Mokudai T, Niwano Y, Kudo T, Suzuki C, Takahashi N, Sato H, Abe T, Niwa T, Ito S, Metabolic alterations by indoxyl sulfate in skeletal muscle induce uremic sarcopenia in chronic kidney disease., Scientific Reports, DOI: 10.1038/srep36618, 6, 36618, 1-13, 2016.11, Sarcopenia is associated with increased morbidity and mortality in chronic kidney disease (CKD). Pathogenic mechanism of skeletal muscle loss in CKD, which is defined as uremic sarcopenia, remains unclear. We found that causative pathological mechanism of uremic sarcopenia is metabolic alterations by uremic toxin indoxyl sulfate. Imaging mass spectrometry revealed indoxyl sulfate accumulated in muscle tissue of a mouse model of CKD. Comprehensive metabolomics revealed that indoxyl sulfate induces metabolic alterations such as upregulation of glycolysis, including pentose phosphate pathway acceleration as antioxidative stress response, via nuclear factor (erythroid-2-related factor)-2. The altered metabolic flow to excess antioxidative response resulted in downregulation of TCA cycle and its effected mitochondrial dysfunction and ATP shortage in muscle cells. In clinical research, a significant inverse association between plasma indoxyl sulfate and skeletal muscle mass in CKD patients was observed. Our results indicate that indoxyl sulfate is a pathogenic factor for sarcopenia in CKD.
10. Kiyonari S, Iimori M, Matsuoka K, Watanabe S, Morikawa-Ichinose T, Miura D, Niimi S, Saeki H, Tokunaga E, Oki E, Morita M, Kadomatsu K, Maehara Y, Kitao H, The1,2-Diaminocyclohexane carrier ligand in oxaliplatin induces p53-dependent transcriptional repression of factors involved in thymidylate biosynthesis., Mol Cancer Ther, DOI: 10.1158/1535-7163.MCT-14-0748, 14, 10, 2332-2342, 2015.07.
11. Morikawa T., Saga H., Hashizume H., Ohta D., CYP710A genes encoding sterol C22-desaturase in Physcomitrella patens as molecular evidence for the evolutionary conservation of a sterol biosynthetic pathway in plants., Planta., 229, 1311-1322, 2009.03, We have characterized cytochromes P450, CYP710A13, and CYP710A14, as the sterol C22-desaturase in the moss Physcomitrella patens. GC-MS analyses demonstrated that P. patens accumulated stigmasterol as the major sterol (56-60% of total sterol) and sitosterol to a lesser extent (8-12%); this sterol profile contrasts with those in higher plants accumulating stigmasterol as a minor component. Recombinant CYP710A13 and CYP710A14 proteins prepared using a baculovirus/insect cell system exhibited the C22-desaturase activity with beta-sitosterol to produce stigmasterol, while campesterol and 24-epi-campesterol were not accepted as the substrates. The K(m) values for beta-sitosterol of CYP710A13 (1.0 +/- 0.043 microM) and CYP710A14 (2.1 +/- 0.17 microM) were at comparable levels of those reported with higher plant CYP710A proteins. In Arabidopsis T87 cells over-expressing CYP710A14, stigmasterol contents reached a level 20- to 72-fold higher than those in the basal level of T87 cells, confirming the C22-desaturase activity of this P450 enzyme. The occurrence of the end-products together with the enzymes involved in the last step of the pathway substantiated the presence of an entire sterol biosynthetic pathway in P. patens, providing evidence for the conservation of the sterol biosynthetic pathway through the evolutionary process of land plants..
12. Morikawa T., Mizutani M., Ohta D., Cytochrome P450 subfamily CYP710A genes encode sterol C-22 desaturase in plants., Biochem Soc Trans., 34, 6, 1202-1205, 2006.09, Sterols are isoprenoid-derived lipids that are produced via the mevalonate pathway and are involved in various cellular functions in eukaryotes such as maintenance of membrane integrity and biosynthetic precursors of steroid hormones. Among cellular sterols, Δ22-sterols containing a double bond at C-22 in the sterol side chain specifically occur in fungi (ergosterol) and plants (stigmasterol and brassicasterol), and several lines of experimental evidence have suggested specific physiological roles of Δ22-sterols in plants. Fungal cytochrome P450 (P450), CYP61, has been established as the sterol C-22 desaturase functioning at the penultimate step in the ergosterol biosynthetic pathway. On the other hand, no particular sequence has been assigned as to the enzyme responsible for the introduction of the double bond into the sterol side chain in plants. In this review, we summarize our recent findings demonstrating that CYP710A P450 family genes encode the plant sterol C-22 desaturases to produce stigmasterol and brassicasterol/crinosterol from β-sitosterol and 24-epi-campesterol respectively..
13. Morikawa T., Mizutani M., Aoki N., Watanabe B., Saga H., Saito S., Oikawa A., Suzuki H., Sakurai N., Shibata D., Wadano A., Sakata K., and Ohta D., Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato., The Plant Cell., 18, 1008-1022, 2006.04, Δ22-Unsaturated sterols, containing a double bond at the C-22 position in the side chain, occur specifically in fungi and plants. Here, we describe the identification and characterization of cytochrome P450s belonging to the CYP710A family as the plant C-22 desaturase. Recombinant proteins of CYP710A1 and CYP710A2 from Arabidopsis thaliana and CYP710A11 from tomato (Lycopersicon esculentum) were expressed using a baculovirus/insect system. The Arabidopsis CYP710A1 and tomato CYP710A11 proteins exhibited C-22 desaturase activity with β-sitosterol to produce stigmasterol (CYP710A1, Km = 1.0 μM and kinetic constant [kcat] = 0.53 min−1; CYP710A11, Km = 3.7 μM and kcat = 10 min−1). In Arabidopsis transgenic lines with CYP710A1 and CYP710A11 overexpression, stigmasterol levels increased by 6- to 32-fold. Arabidopsis CYP710A2 was able to produce brassicasterol and stigmasterol from 24-epi-campesterol and β-sitosterol, respectively. Sterol profiling analyses for CYP710A2 overexpression and a T-DNA insertion event into CYP710A2 clearly demonstrated in planta that CYP710A2 was responsible for both brassicasterol and stigmasterol production. Semiquantitative PCR analyses and promoter:β-glucuronidase transgenic approaches indicated strict tissue/organ-specific regulation for each CYP710A gene, implicating differential tissue distributions of the Δ22-unsaturated sterols in Arabidopsis. Our results support the possibility that the CYP710 family may encode P450s of sterol C-22 desaturases in different organisms..
14. Takubo K., Morikawa T., Nonaka Y., Mizutani M., Takenaka S., Takabe K., Takahashi MA., Ohta D., Identification and molecular characterization of mitochondrial ferredoxins and ferredoxin reductase from Arabidopsis., Plant Mol Biol., 52, 817-830, 2003.04, We have identified and characterized novel types of ferredoxin and ferredoxin reductase from Arabidopsis. Among a number of potential ferredoxin reductase genes in the Arabidopsis genome, AtMFDR was identified to encode a homologue of mitochondrial ferredoxin reductase, and AtMFDX1 and AtMFDX2 were predicted to code for proteins similar to mitochondrial ferredoxin. First, we isolated cDNAs for these proteins and expressed them in heterologous systems of insect cells and Escherichia coli, respectively. The recombinant AtMFDX1 and AtMFDR proteins exhibited spectral properties characteristic of ferredoxin and ferredoxin reductase, respectively, and a pair of recombinant AtMFDX1 and AtMFDR proteins was sufficient to transfer electrons from NAD(P)H to cytochrome c in vitro. Subcellular fractionation analyses suggested membrane association of AtMFDR protein, and protein-gel blot analyses and transient expression studies of green fluorescence protein fusions indicated mitochondrial localization of AtMFDX1 and AtMFDR. RNA-gel blot analyses revealed that the accumulation levels of AtMFDXs and AtMFDR gene transcripts were specifically high in flowers, while protein-gel blot analysis demonstrated substantial accumulation of AtMFDR protein in leaf, stem, and flower. Possible physiological roles of these mitochondrial electron transfer components are discussed in relation to redox dependent metabolic pathways in plants..
1. Ichinose T, Nakamura J, Fujimura Y, Shindo M, Wariishi H, Miura D., Mass Spectrometry imaging of endogenous metabolites in Arabidopsis., Pacifichem 2015, 2015.12.
2. Ichinose T, Fujimura Y, Yamazaki Y, Nakamura J, Wariishi H, Miura D., Visualization of leaf glucosinolate distribution by mass spectrometry imaging in Arabidopsis. , 13th International Symposium on P450 Biodiversity & Biotechnology. , 2016.07.
3. Ichinose T, Fujimura Y, Nakaya S, Yamazaki Y, Nakamura J, Hayakawa E, Wariishi H, Miura D. , Optimal sample preparation method for visualizing global endogenous metabolites by mass spectrometry imaging in Arabidopsis. , 64th ASMS Conference on Mass Spectrometry and allied topics. , 2016.06.
4. Ichinose T, Murayama F, Ishii T, Kawano C, Murayama A, Miki A, Fujimura Y, Yamazaki Y, Wariishi H, Miura D., Establishment of convenient sample preparation method with high sensitivity and excellent reproducibility in mass spectrometry imaging of endogenous primary metabolites., 65th ASMS Conference on Mass Spectrometry and allied topics., 2017.06.
5. Ichinose T, Murayama F, Fujimura Y, Yamazaki Y, Wariishi H, Maruyama A, Miura D. , Visualization of glucosinolate distribution in the inner structure of the leaf by mass spectrometry imaging., 65th ASMS Conference on Mass Spectrometry and allied topics., 2017.06.
6. Ichinose T, Yamazaki Y, Miura D, Maruyama-Nakashita A., Visualization of glucosinolate distribution by mass spectrometry imaging. , Plant Biology 2017., 2017.06.
7. Ichinose T, Yamazaki Y, Miura D, Maruyama-Nakashita A., Spatial distribution of glucosinolates in the inner region of the Arabidopsis leaf., Taiwan-Japan Plant Biology 2017., 2017.11.
8. Ichinose T, Yamazaki Y, Miura D, Maruyama-Nakashita A., Visualization of glucosinolate distribution by mass spectrometry imaging in Arabidopsis., International Symposium on Agricultural, Food, Environmental and Life Sciences in Asia 2017., 2017.11.
9. Ichinose T, Yamazaki Y, Miura D, Maruyama-Nakashita A., Regulation of glucosinolate metabolism by the light conditions in Arabidopsis leaf., 11th International Plant Sulfur Workshop., 2018.09.