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Taniguchi T, Okahashi N, Matsuda F. 13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation. Metab Eng Commun 2024; 18:e00239. [PMID: 38883865 PMCID: PMC11176794 DOI: 10.1016/j.mec.2024.e00239] [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: 01/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Neutrophils are innate immune cells and the first line of defense for the maintenance of homeostasis. However, our knowledge of the metabolic rewiring associated with their differentiation and immune stimulation is limited. Here, quantitative 13C-metabolic flux analysis was performed using HL-60 cells as the neutrophil model. A metabolic model for 13C-metabolic flux analysis of neutrophils was developed based on the accumulation of 13C in intracellular metabolites derived from 13C-labeled extracellular carbon sources and intracellular macromolecules. Aspartate and glutamate in the medium were identified as carbon sources that enter central carbon metabolism. Furthermore, the breakdown of macromolecules, estimated to be fatty acids and nucleic acids, was observed. Based on these results, a modified metabolic model was used for 13C-metabolic flux analysis of undifferentiated, differentiated, and lipopolysaccharide (LPS)-activated HL-60 cells. The glucose uptake rate and glycolytic flux decreased with differentiation, whereas the tricarboxylic acid (TCA) cycle flux remained constant. The addition of LPS to differentiated HL-60 cells activated the glucose uptake rate and pentose phosphate pathway (PPP) flux levels, resulting in an increased rate of total NADPH regeneration, which could be used to generate reactive oxygen species. The flux levels of fatty acid degradation and synthesis were also increased in LPS-activated HL-60 cells. Overall, this study highlights the quantitative metabolic alterations in multiple pathways via the differentiation and activation of HL-60 cells using 13C-metabolic flux analysis.
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Affiliation(s)
- Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Nishimoto K, Okahashi N, Maruyama M, Izumi Y, Nakatani K, Ito Y, Iida J, Bamba T, Matsuda F. Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment. Sci Rep 2023; 13:18549. [PMID: 37899460 PMCID: PMC10613619 DOI: 10.1038/s41598-023-45764-2] [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: 08/14/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023] Open
Abstract
4-hydroxytamoxifen (OHT) is an anti-cancer drug that induces apoptosis in breast cancer cells. Although changes in lipid levels and mitochondrial respiration have been observed in OHT-treated cells, the overall mechanisms underlying these metabolic alterations are poorly understood. In this study, time-series metabolomics and lipidomics were used to analyze the changes in metabolic profiles induced by OHT treatment in the MCF-7 human breast cancer cell line. Lipidomic and metabolomic analyses revealed increases in ceramide, diacylglycerol and triacylglycerol, and decreases in citrate, respectively. Gene expression analyses revealed increased expression of ATP-dependent citrate lyase (ACLY) and subsequent fatty acid biosynthetic enzymes, suggesting that OHT-treated MCF-7 cells activate citrate-to-lipid metabolism. The significance of the observed metabolic changes was evaluated by co-treating MCF-7 cells with OHT and ACLY or a diacylglycerol O-acyltransferase 1 (DGAT1) inhibitor. Co-treatment ameliorated cell death and reduced mitochondrial membrane potential compared to that in OHT treatment alone. The inhibition of cell death by co-treatment with an ACLY inhibitor has been observed in other breast cancer cell lines. These results suggest that citrate-to-lipid metabolism is critical for OHT-induced cell death in breast cancer cell lines.
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Affiliation(s)
- Kazuki Nishimoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
| | - Masaharu Maruyama
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kohta Nakatani
- Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yuki Ito
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Junko Iida
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan.
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Jagadeesh V, Yoshida T, Uraji M, Okahashi N, Matsuda F, Vavricka CJ, Tsuge K, Kondo A. Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM-OGAB Method. ACS Synth Biol 2023; 12:305-318. [PMID: 36563322 DOI: 10.1021/acssynbio.2c00565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recombination of biosynthetic gene clusters including those of non-ribosomal peptide synthetases (NRPSs) is essential for understanding the mechanisms of biosynthesis. Due to relatively huge gene cluster sizes ranging from 10 to 150 kb, the prevalence of sequence repeats, and inability to clearly define optimal points for manipulation, functional characterization of recombinant NRPSs with maintained activity has been hindered. In this study, we introduce a simple yet rapid approach named "Seamed Express Assembly Method (SEAM)" coupled with Ordered Gene Assembly in Bacillus subtilis (OGAB) to reconstruct fully functional plipastatin NRPS. This approach is enabled by the introduction of restriction enzyme sites as seams at module borders. SEAM-OGAB is then first demonstrated by constructing the ppsABCDE NRPS (38.4 kb) to produce plipastatin, a cyclic decapeptide in B. subtilis. The introduced amino acid level seams do not hinder the NRPS function and enable successful production of plipastatin at a commensurable titer. It is challenging to modify the plipastatin NRPS gene cluster due to the presence of three long direct-repeat sequences; therefore, this study demonstrates that SEAM-OGAB can be readily applied towards the recombination of various NRPSs. Compared to previous NRPS gene assembly methods, the advantage of SEAM-OGAB is that it readily enables the shuffling of NRPS gene modules, and therefore, chimeric NRPSs can be rapidly constructed for the production of novel peptides. This chimeric assembly application of SEAM-OGAB is demonstrated by swapping plipastatin NRPS and surfactin NRPS modules to produce two novel lipopeptides in B. subtilis.
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Affiliation(s)
- Varada Jagadeesh
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Misugi Uraji
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Japan.,Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Christopher J Vavricka
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kenji Tsuge
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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Matsuda F, Komori S, Yamada Y, Hara D, Okahashi N. Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules. Mass Spectrom (Tokyo) 2022; 11:A0106. [PMID: 36713802 PMCID: PMC9853114 DOI: 10.5702/massspectrometry.a0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured m/z value is also one of the bottlenecks to narrowing down the candidate compositional formula. In this study, we report that averaging multiple product ion spectra can improve m/z precision as well as the reliability of fragment ions that are observed in such spectra. A graph-based method was applied to cluster a set of similar spectra from multiple DDA data files resulting in creating an averaged product-ion spectrum. The error levels for the m/z values declined following the central limit theorem, which allowed us to reduce the number of candidate compositional formulas. The improved reliability and precision of the averaged spectra will contribute to a more efficient annotation of product ion spectral data.
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Affiliation(s)
- Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan,Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, Japan,Correspondence to: Fumio Matsuda, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan, e-mail:
| | - Shuka Komori
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yuki Yamada
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Daiki Hara
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan,Osaka University Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka, Japan
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