1
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Verkerke ARP, Wang D, Yoshida N, Taxin ZH, Shi X, Zheng S, Li Y, Auger C, Oikawa S, Yook JS, Granath-Panelo M, He W, Zhang GF, Matsushita M, Saito M, Gerszten RE, Mills EL, Banks AS, Ishihama Y, White PJ, McGarrah RW, Yoneshiro T, Kajimura S. BCAA-nitrogen flux in brown fat controls metabolic health independent of thermogenesis. Cell 2024:S0092-8674(24)00346-5. [PMID: 38653240 DOI: 10.1016/j.cell.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/07/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Brown adipose tissue (BAT) is best known for thermogenesis. Rodent studies demonstrated that enhanced BAT thermogenesis is tightly associated with increased energy expenditure, reduced body weight, and improved glucose homeostasis. However, human BAT is protective against type 2 diabetes, independent of body weight. The mechanism underlying this dissociation remains unclear. Here, we report that impaired mitochondrial catabolism of branched-chain amino acids (BCAAs) in BAT, by deleting mitochondrial BCAA carriers (MBCs), caused systemic insulin resistance without affecting energy expenditure and body weight. Brown adipocytes catabolized BCAA in the mitochondria as nitrogen donors for the biosynthesis of non-essential amino acids and glutathione. Impaired mitochondrial BCAA-nitrogen flux in BAT resulted in increased oxidative stress, decreased hepatic insulin signaling, and decreased circulating BCAA-derived metabolites. A high-fat diet attenuated BCAA-nitrogen flux and metabolite synthesis in BAT, whereas cold-activated BAT enhanced the synthesis. This work uncovers a metabolite-mediated pathway through which BAT controls metabolic health beyond thermogenesis.
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Affiliation(s)
- Anthony R P Verkerke
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Dandan Wang
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Naofumi Yoshida
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Zachary H Taxin
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Yuka Li
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Christopher Auger
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Jin-Seon Yook
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Melia Granath-Panelo
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Wentao He
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University, Durham, NC, USA
| | - Guo-Fang Zhang
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Duke University, Durham, NC, USA
| | - Mami Matsushita
- Department of Nutrition, School of Nursing and Nutrition, Tenshi College, Sapporo, Japan
| | - Masayuki Saito
- Laboratory of Biochemistry, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Evanna L Mills
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Phillip J White
- Duke Molecular Physiology Institute, Duke School of Medicine, Department of Medicine, Division of Endocrinology, Metabolism and Nutrition, Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Robert W McGarrah
- Duke Molecular Physiology Institute, Duke School of Medicine, Sarah W. Stedman Nutrition and Metabolism Center, Department of Medicine, Division of Cardiology, Duke University, Durham, NC, USA
| | - Takeshi Yoneshiro
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan; Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA.
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2
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Rrustemi T, Meyer K, Roske Y, Uyar B, Akalin A, Imami K, Ishihama Y, Daumke O, Selbach M. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions. Nat Commun 2024; 15:3146. [PMID: 38605029 PMCID: PMC11009412 DOI: 10.1038/s41467-024-46794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.
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Affiliation(s)
| | - Katrina Meyer
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Bora Uyar
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Oliver Daumke
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.
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3
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Battellino T, Yeung D, Neustaeter H, Spicer V, Ogata K, Ishihama Y, Krokhin OV. Retention time prediction for post-translationally modified peptides: Ser, Thr, Tyr-phosphorylation. J Chromatogr A 2024; 1718:464714. [PMID: 38359688 DOI: 10.1016/j.chroma.2024.464714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
The development of a peptide retention prediction model for reversed-phase chromatography applications in proteomics is reported for peptides carrying phosphorylated Ser, Thr and Tyr-residues. The major retention features have been assessed using a collection of over 10,000 phosphorylated/non-phosphorylated peptide pairs identified in a series 1D and 2D LC-MS/MS acquisitions using formic acid as ion pairing modifier. Single modification event on average results in increased peptide retention for phosphorylation of Ser (+ 1.46), Thr (+1.33), Tyr (+0.93% acetonitrile, ACN) on gradient elution scale for Luna C18(2) stationary phase. We established several composition and sequence specific features, which drive deviations from these average values. Thus, single phosphorylation of serine results in retention shifts ranging from -2.4 to 5.5% ACN depending on position of the residue, nature of nearest neighbour residues, peptide length, hydrophobicity and pI value, and its propensity to form amphipathic helical structures. We established that the altered ion-pairing environment upon phosphorylation is detrimental for this variability. Hydrophobicity of ion-pairing modifier directly informs the magnitude of expected shifts: (most hydrophilic) 0.5 % acetic acid (larger positive shift upon phosphorylation) > 0.1 % formic acid (positive) > 0.1 % trifluoroacetic (negative) > 0.1 % heptafluorobutyric acid (larger negative shift). The effect of phosphorylation has been also evaluated for several separation conditions used in the first dimension of 2D LC applications: high pH reversed-phase (RP), hydrophilic interaction liquid chromatography (HILIC), strong cation- and strong anion exchange separations.
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Affiliation(s)
- Taylor Battellino
- Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg, R3T 2N2, Canada
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 BMSB, 745 Bannatyne Avenue, Winnipeg, R3E 0J9, Canada
| | - Haley Neustaeter
- Department of Chemistry, University of Manitoba, 360 Parker Building, 144 Dysart Road, Winnipeg, R3T 2N2, Canada
| | - Vic Spicer
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada; Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg, R3E 3P4, Canada.
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4
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Tomioka R, Tomioka A, Ogata K, Chan HJ, Chen LY, Guzman UH, Xuan Y, Olsen JV, Chen YJ, Ishihama Y. Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation. J Am Soc Mass Spectrom 2024; 35:386-396. [PMID: 38287222 DOI: 10.1021/jasms.3c00448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
To improve the coverage in bottom-up proteomics, S-aminoethylation of cysteine residues (AE-Cys) was carried out with 2-bromoethylamine, followed by cleavage with lysyl endopeptidase (Lys-C) or Lys-C/trypsin. A model study with bovine serum albumin showed that the C-terminal side of AE-Cys was successfully cleaved by Lys-C. The frequency of side reactions at amino acids other than Cys was less than that in the case of carbamidomethylation of Cys with iodoacetamide. Proteomic analysis of A549 cell extracts in the data-dependent acquisition mode after AE-Cys modification afforded a greater number of identified protein groups, especially membrane proteins. In addition, label-free quantification of proteins in mouse nonsmall cell lung cancer (NSCLC) tissue in the data-independent acquisition mode after AE-Cys modification showed improved NSCLC pathway coverage and greater reproducibility. Furthermore, the AE-Cys method could identify an epidermal growth factor receptor peptide containing the T790 M mutation site, a well-established lung-cancer-related mutation site that has evaded conventional bottom-up methods. Finally, AE-Cys was found to fully mimic Lys in terms of collision-induced dissociation fragmentation, ion mobility separation, and cleavage by Lys-C/trypsin, except for sulfoxide formation during sample preparation.
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Affiliation(s)
- Ryota Tomioka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Biopharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka 561-0825, Osaka, Japan
| | - Ayana Tomioka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hsin-Ju Chan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yu Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ulises H Guzman
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Yue Xuan
- Thermo Fisher Scientific GmbH, Bremen 28199, Germany
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Osaka, Japan
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5
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Nishida H, Kanao E, Ishihama Y. Centrifugal Gel Crushing Tips for Gel-Based Proteome Analysis. Anal Chem 2023; 95:18311-18315. [PMID: 38055789 DOI: 10.1021/acs.analchem.3c02527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We have developed a centrifugal gel-crushing method using a pipet tip. Polyacrylamide gel slices are extruded from the narrowing cavity of a pipet tip by centrifugation in a few minutes to crush them into pieces of appropriate size. The size of the crushed gel could be controlled by several parameters, including centrifugal force and pipet tip cavity. In shotgun proteomics, gel-based LC/MS/MS, so-called GeLC/MS/MS, involves the essential but tedious processes of prefractionation by SDS-PAGE, followed by dicing the entire gel lane into several parts, fine dicing, and in-gel digestion after the diced gel is manually transferred to a microtube. In this study, we developed an alternative way to crush the prefractionated gel slice into optionally small and irregular-shaped gels by centrifugal extrusion of the sliced gel from the narrow cavity of a pipet tip. As a result, we observed improved recovery and reproducibility of digested proteins compared to the conventional method of manual dicing. We believe that this simple and rapid method of crushing polyacrylamide gels, which allows for parallel operations and automation, is useful for GeLC/MS/MS analysis and applicable to other approaches, including top-down proteomics.
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Affiliation(s)
- Hiroshi Nishida
- Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Kanao
- Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Yasushi Ishihama
- Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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6
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Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
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Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
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7
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Tsumagari K, Isobe Y, Ishihama Y, Seita J, Arita M, Imami K. Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics. Mol Cell Proteomics 2023; 22:100677. [PMID: 37949301 PMCID: PMC10696250 DOI: 10.1016/j.mcpro.2023.100677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/11/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Proteins can be modified by lipids in various ways, for example, by myristoylation, palmitoylation, farnesylation, and geranylgeranylation-these processes are collectively referred to as lipidation. Current chemical proteomics using alkyne lipids has enabled the identification of lipidated protein candidates but does not identify endogenous lipidation sites and is not readily applicable to in vivo systems. Here, we introduce a proteomic methodology for global analysis of endogenous protein N-terminal myristoylation sites that combines liquid-liquid extraction of hydrophobic lipidated peptides with liquid chromatography-tandem mass spectrometry using a gradient program of acetonitrile in the high concentration range. We applied this method to explore myristoylation sites in HeLa cells and identified a total of 75 protein N-terminal myristoylation sites, which is more than the number of high-confidence myristoylated proteins identified by myristic acid analog-based chemical proteomics. Isolation of myristoylated peptides from HeLa digests prepared with different proteases enabled the identification of different myristoylated sites, extending the coverage of N-myristoylome. Finally, we analyzed in vivo myristoylation sites in mouse tissues and found that the lipidation profile is tissue-specific. This simple method (not requiring chemical labeling or affinity purification) should be a promising tool for global profiling of protein N-terminal myristoylation.
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Affiliation(s)
- Kazuya Tsumagari
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yosuke Isobe
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yasushi Ishihama
- Department of Molecular Systems Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Ibaraki, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan; Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
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8
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Niinae T, Sugiyama N, Ishihama Y. Validity of the cell-extracted proteome as a substrate pool for exploring phosphorylation motifs of kinases. Genes Cells 2023; 28:727-735. [PMID: 37658684 DOI: 10.1111/gtc.13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
Three representative protein kinases with different substrate preferences, ERK1 (Pro-directed), CK2 (acidophilic), and PKA (basophilic), were used to investigate phosphorylation sequence motifs in substrate pools consisting of the proteomes from three different cell lines, MCF7 (human mammary carcinoma), HeLa (human cervical carcinoma), and Jurkat (human acute T-cell leukemia). Specifically, recombinant kinases were added to the cell-extracted proteomes to phosphorylate the substrates in vitro. After trypsin digestion, the phosphopeptides were enriched and subjected to nanoLC/MS/MS analysis to identify their phosphorylation sites on a large scale. By analyzing the obtained phosphorylation sites and their surrounding sequences, phosphorylation motifs were extracted for each kinase-substrate proteome pair. We found that each kinase exhibited the same set of phosphorylation motifs, independently of the substrate pool proteome. Furthermore, the identified motifs were also consistent with those found using a completely randomized peptide library. These results indicate that cell-extracted proteomes can provide kinase phosphorylation motifs with sufficient accuracy, even though their sequences are not completely random, supporting the robustness of phosphorylation motif identification based on phosphoproteome analysis of cell extracts as a substrate pool for a kinase of interest.
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Affiliation(s)
- Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
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9
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Kanao E, Ishida K, Mizuta R, Li Y, Imami K, Tanigawa T, Sasaki Y, Akiyoshi K, Adachi J, Otsuka K, Ishihama Y, Kubo T. Rapid and Highly Efficient Purification of Extracellular Vesicles Enabled by a TiO 2 Hybridized Spongy-like Polymer. Anal Chem 2023; 95:14502-14510. [PMID: 37703188 DOI: 10.1021/acs.analchem.3c03411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
We developed a novel purification medium of extracellular vesicles (EVs) by constructing a spongy-like monolithic polymer kneaded with TiO2 microparticles (TiO2-hybridized spongy monolith, TiO2-SPM). TiO2-SPM was applied in a solid-phase extraction format and enabled simple, rapid, and highly efficient purification of EVs. This is due to the high permeability caused by the continuous large flow-through pores of the monolithic skeleton (median pore size; 5.21 μm) and the specific interaction of embedded TiO2 with phospholipids of the lipid bilayers. Our method also excels in efficiency and comprehensiveness, collecting small EVs (SEVs) from the same volume of a cell culture medium 130.7 times more than typical ultracentrifugation and 4.3 times more than affinity purification targeting surface phosphatidylserine by magnetic beads. The purification method was completed within 1 h with simple operations and was directly applied to serum SEVs. Finally, we demonstrated flexibility toward the shape and size of our method by depleting EVs from fetal bovine serum (FBS), which is a necessary process to prevent contamination of culture cell-derived EVs with exogenous FBS-derived EVs. Our method will eliminate the tedious and difficult purification processes of EVs, providing a universal purification platform for EV-based drug discovery and pathological diagnosis.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Osaka, Japan
| | - Koki Ishida
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ryosuke Mizuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuka Li
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Tetsuya Tanigawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Jun Adachi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Osaka, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki 567-0085, Osaka, Japan
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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10
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Li Y, Kanao E, Yamano T, Ishihama Y, Imami K. TurboID-EV: Proteomic Mapping of Recipient Cellular Proteins Proximal to Small Extracellular Vesicles. Anal Chem 2023; 95:14159-14164. [PMID: 37709279 PMCID: PMC10534987 DOI: 10.1021/acs.analchem.3c01015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Extracellular vesicles (EVs), including exosomes, have been recognized as key mediators of intercellular communications through donor EV and recipient cell interaction. Until now, most studies have focused on the development of analytical tools to separate EVs and their applications for the molecular profiling of EV cargo. However, we lack a complete picture of the mechanism of EV uptake by the recipient cells. Here, we developed the TurboID-EV system with the engineered biotin ligase TurboID, tethered to the EV membrane, which allowed us to track the footprints of EVs during and after EV uptake by the proximity-dependent biotinylation of recipient cellular proteins. To analyze biotinylated recipient proteins from low amounts of input cells (corresponding to ∼10 μg of proteins), we developed an integrated proteomic workflow that combined stable isotope labeling with amino acids in cultured cells (SILAC), fluorescence-activated cell sorting, spintip-based streptavidin affinity purification, and mass spectrometry. Using this method, we successfully identified 456 biotinylated recipient proteins, including not only well-known proteins involved in endocytosis and macropinocytosis but also other membrane-associated proteins such as desmoplakin and junction plakoglobin. The TurboID-EV system should be readily applicable to various EV subtypes and recipient cell types, providing a promising tool to dissect the specificity of EV uptake mechanisms on a proteome-wide scale.
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Affiliation(s)
- Yuka Li
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Kanao
- Laboratory
of Clinical and Analytical Chemistry, National
Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
- Department
of Proteomics and Drug Discovery, Graduate School of Pharmaceutical
Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoyoshi Yamano
- Department
of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1164, Japan
- WPI
Nano Life Science Institute (NanoLSI), Kanazawa
University, Kanazawa 920-1164, Japan
| | - Yasushi Ishihama
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory
of Clinical and Analytical Chemistry, National
Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
- Department
of Proteomics and Drug Discovery, Graduate School of Pharmaceutical
Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Koshi Imami
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- PRESTO,
Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0075, Japan
- Proteome
Homeostasis Research Unit, RIKEN Center
for Integrative Medical Sciences, Yokohama 230-0045, Japan
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11
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Grey AC, Lin Q, Low TY, Wu W, Haynes PA, Chung MCM, Chen YJ, Cordwell SJ, Ishihama Y, Xu P, Hoffmann P, Kwon HJ, Poon TCW. 11th Asia Oceania Human Proteome Organization Congress Report. Mol Cell Proteomics 2023; 22:100627. [PMID: 37532177 PMCID: PMC10472285 DOI: 10.1016/j.mcpro.2023.100627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023] Open
Abstract
As the first in-person Asia Oceania Human Proteomics Organization (AOHUPO) congress since 2018, the 11th AOHUPO congress was an opportune time for the research community to reconnect and to renew friendships after the long period of restricted travel due to the global pandemic. Moreover, this congress was a great opportunity for the many AO regional proteomics and mass spectrometry scientists to meet in Singapore to exchange ideas and to present their latest findings. Cohosted by the Singapore Society for Mass Spectrometry and the Malaysian Proteomics Society and held in conjunction with the seventh Asia Oceania Agricultural Proteomics Organization Congress and Singapore Society for Mass Spectrometry 2023, the meeting featured both human and agricultural proteomics. Over five hundred scientists from the AO region converged on the MAX Atria @ Singapore EXPO, Changi, Singapore from May 8 to 10 for the main congress. The diverse program was made up of 64 invited speakers and panellists for seven plenary lectures, 27 concurrent symposia, precongress and postcongress workshops, and 174 poster presentations. The AOHUPO society were able to celebrate not only their 20th anniversary but also the outstanding academic research from biological and agricultural proteomics and related 'omics fields being conducted across the Asia-Oceania region.
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Affiliation(s)
- Angus C Grey
- Department of Physiology, University of Auckland, Auckland, New Zealand.
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Wei Wu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), and Department of Pharmacy, National University of Singapore, Singapore
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, Nova Scotia, Australia
| | - Maxey C M Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Stuart J Cordwell
- School of Life and Environmental Sciences and Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Peter Hoffmann
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Initiative, Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Terence C W Poon
- Pilot Laboratory, Proteomics Core, Institute of Translational Medicine, Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
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12
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Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun 2023; 14:3599. [PMID: 37328457 PMCID: PMC10276052 DOI: 10.1038/s41467-023-39347-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
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Affiliation(s)
- Ana Martínez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kyle Fort
- Thermo Fisher Scientific, Bremen, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Yue Xuan
- Thermo Fisher Scientific, Bremen, Germany.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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13
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Kanao E, Osaki H, Tanigawa T, Takaya H, Sano T, Adachi J, Otsuka K, Ishihama Y, Kubo T. Rational Supramolecular Strategy via Halogen Bonding for Effective Halogen Recognition in Molecular Imprinting. Anal Chem 2023. [PMID: 37230938 DOI: 10.1021/acs.analchem.3c01311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Halogen bonding is a highly directional interaction and a potential tool in functional material design through self-assembly. Herein, we describe two fundamental supramolecular strategies to synthesize molecularly imprinted polymers (MIPs) with halogen bonding-based molecular recognition sites. In the first method, the size of the σ-hole was increased by aromatic fluorine substitution of the template molecule, enhancing the halogen bonding in the supramolecule. The second method involved sandwiching hydrogen atoms of a template molecule between iodo substituents, which suppressed competing hydrogen bonding and enabled multiple recognition patterns, improving the selectivity. The interaction mode between the functional monomer and the templates was elucidated by 1H NMR, 13C NMR, X-ray absorption spectroscopy, and computational simulation. Finally, we succeeded in the effective chromatographic separation of diiodobenzene isomers on the uniformly sized MIPs prepared by multi-step swelling and polymerization. The MIPs selectively recognized halogenated thyroid hormones via halogen bonding and could be applied to screening endocrine disruptors.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Hayato Osaki
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tetsuya Tanigawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hikaru Takaya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoharu Sano
- Center for Environmental Measurement and Analysis, National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki 305-8506, Japan
| | - Jun Adachi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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14
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Narukawa Y, Sugiyama N, Miura J, Yamashita R, Tominaga S, Izumi Y, Bamba T, Ishihama Y, Kashiwagi Y, Murakami S. Chronic hyperglycemia reduces the expression of intercellular adhesion molecules and increases intercellular hyperpermeability in the periodontal epithelium. J Periodontal Res 2023. [PMID: 37221815 DOI: 10.1111/jre.13140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 03/31/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND/AIMS Hyperglycemia in diabetes is closely associated with periodontal disease progression. This study aimed to investigate the effect of hyperglycemia on the barrier function of gingival epithelial cells as a cause of hyperglycemia-exacerbated periodontitis in diabetes mellitus. METHODS The abnormal expression of adhesion molecules in gingival epithelium in diabetes was compared between db/db and control mice. To study the effects of hyperglycemia on interepithelial cell permeability, the mRNA and protein expressions of adhesion molecules were investigated using a human gingival epithelial cell line (epi 4 cells) in the presence of either 5.5 mM glucose (NG) or 30 mM glucose (HG). Immunocytochemical and histological analyses were performed. We also studied HG-related intracellular signaling to assess abnormal adhesion molecule expression in the cultured epi 4 cells. RESULTS The results of the proteomic analysis implied the abnormal regulation of cell-cell adhesion, and mRNA and protein expression assessments revealed the significant downregulation of Claudin1 expression in the gingival tissues of db/db mice (p < .05 vs control). Similarly, the mRNA and protein expressions of adhesion molecules were lower in epi 4 cells cultured under HG conditions than in those cultured under NG conditions (p < .05). Three-dimensional culture and transmission electron microscopy revealed reduced thickness of the epithelial cell layers with no flattened apical cells and heterogeneously arranged intercellular spaces among adjacent epi 4 cells under the HG. These results were consistent with the increased permeability of epi 4 cells under the HG relative to that of cells under the NG. This abnormal expression of intercellular adhesion molecules under the HG was related to the increased expression of receptors for advanced glycation end products (AGEs) and oxidative stress relative to that seen under the NG, along with stimulation of ERK1/2 phosphorylation in epi 4 cells. CONCLUSIONS High glucose-induced impairment of intercellular adhesion molecule expression in gingival epithelial cells was related to the intercellular permeability of gingival cells, representing a possible link to hyperglycemia-related AGE signaling, oxidative stress, and ERK1/2 activation.
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Affiliation(s)
- Yuki Narukawa
- Department of Periodontology, Division of Oral Biology and Disease Control, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Jiro Miura
- Division of Interdisciplinary Dentistry, Osaka University Dental Hospital, Osaka, Japan
| | - Rentaro Yamashita
- Division of Interdisciplinary Dentistry, Osaka University Dental Hospital, Osaka, Japan
| | - Shotaro Tominaga
- Department of Periodontology, Division of Oral Biology and Disease Control, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yoichiro Kashiwagi
- Department of Periodontology, Division of Oral Biology and Disease Control, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Shinya Murakami
- Department of Periodontology, Division of Oral Biology and Disease Control, Osaka University Graduate School of Dentistry, Osaka, Japan
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15
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Kitagori K, Oku T, Wakabayashi M, Nakajima T, Nakashima R, Murakami K, Hirayama Y, Ishihama Y, Ohmura K, Morinobu A, Mimori T, Yoshifuji H. Expression of S100A8 protein on B cells is associated with disease activity in patients with systemic lupus erythematosus. Arthritis Res Ther 2023; 25:76. [PMID: 37165399 PMCID: PMC10170829 DOI: 10.1186/s13075-023-03057-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an intractable disease characterized by autoantibody production and autoreactive B and T cell proliferation. Although several studies have revealed multiple genetic and environmental associations, the underlying mechanisms remain unknown. METHODS We performed proteomics and transcriptomics using liquid chromatography-mass spectrometry and DNA microarray, using peripheral blood B cells from patients with SLE, and healthy controls (HC). We explored molecules associated with the pathophysiology of SLE by flow cytometry and B cell stimulation assay. RESULTS We identified for the first time that expression of both S100A8 protein and mRNA were markedly upregulated in SLE B cells. The results obtained using flow cytometry showed that S100A8 was highly expressed on the surface of B cells of patients with active SLE (MFI; HC 102.5 ± 5.97, stable SLE 111.4 ± 12.87, active SLE 586.9 ± 142.9), and S100A8 on the cell surface was decreased after treatment (MFI; pre-treat 1094.5 ± 355.38, post-treat 492.25 ± 247.39); therefore, it is suggested that S100A8 may be a marker for disease activity. The mRNA expression of S100A8 was particularly upregulated in memory B cells of SLE (56.68 fold higher than HC), suggesting that S100A8 may be mainly secreted by memory B cells in the pathogenesis of SLE. CONCLUSIONS Our results imply that the S100A8 proteins secreted from memory B cells may stimulate granulocytes and monocytes through pattern recognition receptors, activate the innate immune system, and are involved in the pathogenesis of SLE.
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Affiliation(s)
- Koji Kitagori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuma Oku
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Portfolio & Science, Astellas Pharma Inc, Tokyo, Japan
| | - Masaki Wakabayashi
- Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Tomoya Nakajima
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ran Nakashima
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosaku Murakami
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Hirayama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Portfolio & Science, Astellas Pharma Inc, Tokyo, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | | | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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16
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Komori Y, Niinae T, Imami K, Yanagibayashi J, Yasunaga K, Imamura S, Tomita M, Ishihama Y. Bioinertization of nanoLC/MS/MS systems by depleting metal ions from the mobile phases for phosphoproteomics. Mol Cell Proteomics 2023; 22:100535. [PMID: 36958626 PMCID: PMC10172917 DOI: 10.1016/j.mcpro.2023.100535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/16/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
We have successfully developed a bioinertized nanoflow liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS) system for the highly sensitive analysis of phosphopeptides by depleting metal ions from the mobile phase. We found that not only direct contact of phosphopeptides with metal components, but also indirect contact with nanoLC pumps through the mobile phase causes significant losses during the recovery of phosphopeptides. Moreover, electrospray ionization was adversely affected by the mobile phase containing multiple metal ions as well as by the sample solvents contaminated with metal ions used in immobilized metal ion affinity chromatography for phosphopeptide enrichment. To solve these problems, metal ions were depleted by inserting an on-line metal ion removal device containing metal-chelating membranes between the gradient mixer and the autosampler. As a result, the peak areas of the identified phosphopeptides increased an average of 9.9-fold overall and 77-fold for multiply phosphorylated peptides with the insertion of the on-line metal ion removal system. This strategy would be applicable to highly sensitive analysis of other phosphorylated biomolecules by microscale-LC/MS/MS.
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Affiliation(s)
- Yumi Komori
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan; RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | | | | | | | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
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17
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Imami K, Selbach M, Ishihama Y. Monitoring mitochondrial translation by pulse SILAC. J Biol Chem 2023; 299:102865. [PMID: 36603763 PMCID: PMC9922817 DOI: 10.1016/j.jbc.2022.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial ribosomes are specialized to translate the 13 membrane proteins encoded in the mitochondrial genome, which shapes the oxidative phosphorylation complexes essential for cellular energy metabolism. Despite the importance of mitochondrial translation (MT) control, it is challenging to identify and quantify the mitochondrial-encoded proteins because of their hydrophobic nature and low abundance. Here, we introduce a mass spectrometry-based proteomic method that combines biochemical isolation of mitochondria with pulse stable isotope labeling by amino acids in cell culture. Our method provides the highest protein identification rate with the shortest measurement time among currently available methods, enabling us to quantify 12 of the 13 mitochondrial-encoded proteins. We applied this method to uncover the global picture of (post-)translational regulation of both mitochondrial- and nuclear-encoded subunits of oxidative phosphorylation complexes. We found that inhibition of MT led to degradation of orphan nuclear-encoded subunits that are considered to form subcomplexes with the mitochondrial-encoded subunits. This method should be readily applicable to study MT programs in many contexts, including oxidative stress and mitochondrial disease.
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Affiliation(s)
- Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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18
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Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver J, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman B, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss M, Zhu Y, Ishihama Y, Vizcaíno J. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res 2023; 51:D1539-D1548. [PMID: 36370099 PMCID: PMC9825490 DOI: 10.1093/nar/gkac1040] [Citation(s) in RCA: 126] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
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Affiliation(s)
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Jeremy J Carver
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Luis Mendoza
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Deepti J Kundu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shengbo Wang
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chakradhar Bandla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Selvakumar Kamatchinathan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suresh Hewapathirana
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Julie Wertz
- Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Dept. Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle WA 98109, USA
| | - Shin Kawano
- Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan
- School of Frontier Engineering, Kitasato University, Sagamihara 252-0373, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yu Watanabe
- Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | | | | | - Yunping Zhu
- Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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19
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Battellino T, Ogata K, Spicer V, Ishihama Y, Krokhin O. Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid. J Proteome Res 2023; 22:272-278. [PMID: 36480176 DOI: 10.1021/acs.jproteome.2c00388] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the general acceptance of formic acid as the additive of choice for peptide reversed-phase LC-MS/MS applications, some still argue that the selection of acetic acid represents a better option. To settle this debate, we investigated both the difference in MS sensitivity and chromatographic behavior of peptides between these two systems. This interlaboratory study was performed using different MS setups and C18 separation media employing both 0.1% formic and 0.5% acetic acid as ion pairing modifiers. Relative to formic acid, we find an overall ∼2.2-2.5× increase in MS signal and a slight decrease in RP LC retention (-0.7% acetonitrile on average) for acetic acid conditions. While these two features have opposing effects on peptide detectability, we find that acetic acid produces up to 60% higher peptide ID output depending on the type of sample. The drop in RPLC retention increases with peptide net charge at acidic pH. MS signal is dependent on the difference between the charge of the precursor ion and the charge of the peptide in solution, favoring species with a low pI. Lower peptide retention under acetic acid conditions demonstrates its higher hydrophilicity and, as expected, leads to composition and sequence-dependent character of the observed retention shift.
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Affiliation(s)
- Taylor Battellino
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada.,University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
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20
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Kanao E, Wada S, Nishida H, Kubo T, Tanigawa T, Imami K, Shimoda A, Umezaki K, Sasaki Y, Akiyoshi K, Adachi J, Otsuka K, Ishihama Y. Classification of Extracellular Vesicles Based on Surface Glycan Structures by Spongy-like Separation Media. Anal Chem 2022; 94:18025-18033. [PMID: 36511577 DOI: 10.1021/acs.analchem.2c04391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles (EVs) are lipid bilayer vesicles that enclose various biomolecules. EVs hold promise as sensitive biomarkers to detect and monitor various diseases. However, they have heterogeneous molecular compositions. The compositions of EVs from identical donor cells obtained using the same purification methods may differ, which is a significant obstacle for elucidating objective biological functions. Herein, the potential of a novel lectin-based affinity chromatography (LAC) method to classify EVs based on their glycan structures is demonstrated. The proposed method utilizes a spongy-like monolithic polymer (spongy monolith, SPM), which consists of poly(ethylene-co-glycidyl methacrylate) with continuous micropores and allows an efficient in situ protein reaction with epoxy groups. Two distinct lectins with different specificities, Sambucus sieboldiana agglutinin and concanavalin A, are effectively immobilized on SPM without impacting the binding activity. Moreover, high recovery rates of liposomal nanoparticles as a model of EVs are achieved due to the large flow-through pores (>10 μm) of SPM compared to a typical agarose gel. Finally, lectin-immobilized SPMs are employed to classify EVs based on the surface glycan structures and demonstrate different subpopulations by proteome profiling. This is the first approach to clarify the variation of protein contents in EVs by the difference of surface glycans via lectin immobilized media.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Shuntaro Wada
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Hiroshi Nishida
- National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Tetsuya Tanigawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama332-0012, Japan
| | - Asako Shimoda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Kaori Umezaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Jun Adachi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto615-8510, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto606-8501, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka567-0085, Japan
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21
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Ogata K, Takagi S, Sugiyama N, Ishihama Y. Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors. Cancers (Basel) 2022; 15:cancers15010078. [PMID: 36612075 PMCID: PMC9817674 DOI: 10.3390/cancers15010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We present a motif-targeting phosphoproteome analysis workflow utilizing in vitro kinase reaction to enrich a subset of peptides with specific primary sequence motifs. Phosphopeptides are enriched and dephosphorylated with alkaline phosphatase, followed by in vitro kinase reaction to phosphorylate substrate peptides with specific primary-sequence motifs. These phosphopeptides are enriched again, TMT-labeled, dephosphorylated to enhance MS-detectability, and analyzed by LC/MS/MS. We applied this approach to inhibitor-treated cancer cells, and successfully profiled the inhibitory spectra of multiple kinase inhibitors. We anticipate this approach will be applicable to target specific subsets of the phosphoproteome using the wide variety of available recombinant protein kinases.
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22
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Namiki J, Suzuki S, Shibata S, Kubota Y, Kaneko N, Yoshida K, Yamaguchi R, Matsuzaki Y, Masuda T, Ishihama Y, Sawamoto K, Okano H. Chitinase-like protein 3: A novel niche factor for mouse neural stem cells. Stem Cell Reports 2022; 17:2704-2717. [PMID: 36368330 PMCID: PMC9768575 DOI: 10.1016/j.stemcr.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022] Open
Abstract
The concept of a perivascular niche has been proposed for neural stem cells (NSCs). This study examined endothelial colony-forming cell (ECFC)-secreted proteins as potential niche factors for NSCs. Intraventricle infusion with ECFC-secreted proteins increased the number of NSCs. ECFC-secreted proteins were more effective in promoting NSC self-renewal than marrow stromal cell (MSC)-secreted proteins. Differential proteomics analysis of MSC-secreted and ECFC-secreted proteins was performed, which revealed chitinase-like protein 3 (CHIL3; also called ECF-L or Ym1) as a candidate niche factor for NSCs. Experiments with recombinant CHIL3, small interfering RNA, and neutralizing antibodies demonstrated that CHIL3 stimulated NSC self-renewal with neurogenic propensity. CHIL3 was endogenously expressed in the neurogenic niche of the brain and retina as well as in the injured brain and retina. Transcriptome and phosphoproteome analyses revealed that CHIL3 activated various genes and proteins associated with NSC maintenance or neurogenesis. Thus, CHIL3 is a novel niche factor for NSCs.
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Affiliation(s)
- Jun Namiki
- Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Corresponding author
| | - Sayuri Suzuki
- Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shinsuke Shibata
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yoshiaki Kubota
- Department of Anatomy, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Naoko Kaneko
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Kenji Yoshida
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Sumitomo Pharma Co. Ltd., Osaka, Osaka 541-0045, Japan
| | - Ryo Yamaguchi
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Sumitomo Pharma Co. Ltd., Osaka, Osaka 541-0045, Japan
| | - Yumi Matsuzaki
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Yasushi Ishihama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazunobu Sawamoto
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan,Corresponding author
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23
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Low TY, Chen YJ, Ishihama Y, Chung MCM, Cordwell S, Poon TCW, Kwon HJ. The Second Asia-Oceania Human Proteome Organization (AOHUPO) Online Education Series on the Renaissance of Clinical Proteomics: Biomarkers, Imaging and Therapeutics. Mol Cell Proteomics 2022; 21:100436. [PMID: 36309314 PMCID: PMC9700300 DOI: 10.1016/j.mcpro.2022.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
In 2021, the Asia-Oceania Human Proteome Organization (AOHUPO) initiated a new endeavor named the AOHUPO Online Education Series with the aim to promote scientific education and collaboration, exchange of ideas and culture among the young scientists in the AO region. Following the warm participation, the AOHUPO organized the second series in 2022, with the theme "The Renaissance of Clinical Proteomics: Biomarkers, Imaging and Therapeutics". This time, the second AOHUPO Online Education Series was hosted by the UKM Medical Molecular Biology Institute (UMBI) affiliated to the National University of Malaysia (UKM) in Kuala Lumpur, Malaysia on three consecutive Fridays (11th, 18th and 25th of March). More than 300 participants coming from 29 countries/regions registered for this 3-days event. This event provided an amalgamation of six prominent speakers and all participants whose interests lay mainly in applying MS-based and non-MS-based proteomics for clinical investigation.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Max Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stuart Cordwell
- School of Life and Environmental Sciences and Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
| | - Terence Chuen Wai Poon
- Pilot Laboratory, Proteomics Core, Institute of Translational Medicine, Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Ho Jeong Kwon
- Chemical Genomics Leader Research Initiative, Department of Biotechnology, Yonsei University, Seoul, South Korea,For correspondence: Ho Jeong Kwon
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24
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Ishihama Y, Fukumoto K, Watanabe R, Nakatani S, Tsuda A, Otoshi T, Yamada K, Yamada S, Negoro N, Emoto M, Hashimoto M. Retroperitoneal fibrosis requiring prompt nephrostomy in a case with immunoglobulin A vasculitis. Scand J Rheumatol 2022; 51:419-421. [PMID: 35658823 DOI: 10.1080/03009742.2022.2047312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Y Ishihama
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - K Fukumoto
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - R Watanabe
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - S Nakatani
- Department of Metabolism, Endocrinology, and Molecular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - A Tsuda
- Department of Metabolism, Endocrinology, and Molecular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - T Otoshi
- Department of Urology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - K Yamada
- Department of Dermatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - S Yamada
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - N Negoro
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - M Emoto
- Department of Metabolism, Endocrinology, and Molecular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - M Hashimoto
- Department of Clinical Immunology, Osaka City University Graduate School of Medicine, Osaka, Japan
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25
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Chong YK, Tartey S, Yoshikawa Y, Imami K, Li S, Yoshinaga M, Hirabayashi A, Liu G, Vandenbon A, Hia F, Uehata T, Mino T, Suzuki Y, Noda T, Ferrandon D, Standley DM, Ishihama Y, Takeuchi O. Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism. Sci Signal 2022; 15:eabm5011. [PMID: 35412849 DOI: 10.1126/scisignal.abm5011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Toll-like receptor (TLR) stimulation induces glycolysis and the production of mitochondrial reactive oxygen species (ROS), both of which are critical for inflammatory responses in macrophages. Here, we demonstrated that cyclin J, a TLR-inducible member of the cyclin family, reduced cytokine production in macrophages by coordinately controlling glycolysis and mitochondrial functions. Cyclin J interacted with cyclin-dependent kinases (CDKs), which increased the phosphorylation of a subset of CDK substrates, including the transcription factor FoxK1 and the GTPase Drp1. Cyclin J-dependent phosphorylation of FoxK1 decreased the transcription of glycolytic genes and Hif-1α activation, whereas hyperactivation of Drp1 by cyclin J-dependent phosphorylation promoted mitochondrial fragmentation and impaired the production of mitochondrial ROS. In mice, cyclin J in macrophages limited the growth of tumor xenografts and protected against LPS-induced shock but increased the susceptibility to bacterial infection. Collectively, our findings indicate that cyclin J-CDK signaling promotes antitumor immunity and the resolution of inflammation by opposing the metabolic changes that drive inflammatory responses in macrophages.
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Affiliation(s)
- Yee Kien Chong
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sarang Tartey
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,IGM Biosciences Inc., Mountain View, CA, USA
| | - Yuki Yoshikawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Guohao Liu
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | | | - Daron M Standley
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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26
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Kanao E, Nakano K, Kamei R, Hosomi T, Ishihama Y, Adachi J, Kubo T, Otsuka K, Yanagida T. Moderate molecular recognitions on ZnO m-plane and their selective capture/release of bio-related phosphoric acids. Nanoscale Adv 2022; 4:1649-1658. [PMID: 36134362 PMCID: PMC9417451 DOI: 10.1039/d1na00865j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/16/2022] [Indexed: 05/25/2023]
Abstract
Herein, we explore the hidden molecular recognition abilities of ZnO nanowires uniformly grown on the inner surface of an open tubular fused silica capillary via liquid chromatography. Chromatographic evaluation revealed that ZnO nanowires showed a stronger intermolecular interaction with phenylphosphoric acid than any other monosubstituted benzene. Furthermore, ZnO nanowires specifically recognized the phosphate groups present in nucleotides even in the aqueous mobile phase, and the intermolecular interaction increased with the number of phosphate groups. This discrimination of phosphate groups in nucleotides was unique to the rich (101̄0) m-plane of ZnO nanowires with a moderate hydrophilicity and negative charge. The discrimination could be evidenced by the changes in the infrared bands of the phosphate groups on nucleotides on ZnO nanowires. Finally, as an application of the molecular recognition, nucleotides were separated by the number of phosphate groups, utilizing optimized gradient elution on ZnO nanowire column. Thus, the present results elucidate the unique and versatile molecular selectivity of well-known ZnO nanostructures for the capture and separation of biomolecules.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan +81-75-753-4601 +81-75-753-4565
- National Institutes of Bio Medical Innovation, Health and Nutrition Ibaraki Osaka 567-0085 Japan
| | - Katsuya Nakano
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan +81-75-383-2450 +81-75-383-2448
| | - Ryoma Kamei
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
| | - Takuro Hosomi
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan +81-75-753-4601 +81-75-753-4565
- National Institutes of Bio Medical Innovation, Health and Nutrition Ibaraki Osaka 567-0085 Japan
| | - Jun Adachi
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo-ku Kyoto 606-8501 Japan +81-75-753-4601 +81-75-753-4565
- National Institutes of Bio Medical Innovation, Health and Nutrition Ibaraki Osaka 567-0085 Japan
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan +81-75-383-2450 +81-75-383-2448
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University Katsura, Nishikyo-ku Kyoto 615-8510 Japan +81-75-383-2450 +81-75-383-2448
| | - Takeshi Yanagida
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8654 Japan
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27
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Shinkawa Y, Imami K, Fuseya Y, Sasaki K, Ohmura K, Ishihama Y, Morinobu A, Iwai K. ABIN1 is a signal-induced autophagy receptor that attenuates NF-κB activation by recognizing linear ubiquitin chains. FEBS Lett 2022; 596:1147-1164. [PMID: 35213742 DOI: 10.1002/1873-3468.14323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/03/2022] [Accepted: 02/15/2022] [Indexed: 11/09/2022]
Abstract
Linear ubiquitin chains play pivotal roles in immune signaling by augmenting NF-κB activation and suppressing programmed cell death induced by various stimuli. A20-binding inhibitor of NF-κB 1 (ABIN1) binds to linear ubiquitin chains and attenuates NF-κB activation and cell death induction. Although interactions with linear ubiquitin chains are thought to play a role in ABIN1-mediated suppression of NF-κB and cell death, the underlying molecular mechanisms remain unclear. Here, we show that upon stimulation by Toll-like receptor (TLR) ligands, ABIN1 is phosphorylated on Ser 83 and functions as a selective autophagy receptor. ABIN1 recognizes components of the MyD88 signaling complex via interaction with linear ubiquitin chains conjugated to components of the complex in TLR signaling, which leads to autophagic degradation of signaling proteins and attenuated NF-κB signaling. Our current findings indicate that phosphorylation and linear ubiquitination also play a role in downregulation of signaling via selective induction of autophagy.
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Affiliation(s)
- Yutaka Shinkawa
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasuhiro Fuseya
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsuhiro Sasaki
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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28
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. Cell Rep Methods 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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29
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Liu JY, Inoshita T, Shiba-Fukushima K, Yoshida S, Ogata K, Ishihama Y, Imai Y, Hattori N. OUP accepted manuscript. Hum Mol Genet 2022; 31:2623-2638. [PMID: 35313349 PMCID: PMC9396936 DOI: 10.1093/hmg/ddac064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial kinase PTEN-induced kinase 1 (PINK1) and cytosolic ubiquitin ligase (E3) Parkin/PRKN are involved in mitochondrial quality control responses. PINK1 phosphorylates ubiquitin and the Parkin ubiquitin-like (Ubl) domain at serine 65 and promotes Parkin activation and translocation to damaged mitochondria. Upon Parkin activation, the Ubl domain is ubiquitinated at lysine (K) 27 and K48 residues. However, the contribution of K27/K48 ubiquitination toward Parkin activity remains unclear. In this study, ubiquitination of K56 (corresponding to K27 in the human), K77 (K48 in the human) or both was blocked by generating Drosophila Parkin (dParkin) mutants to examine the effects of Parkin Ubl domain ubiquitination on Parkin activation in Drosophila. The dParkin, in which K56 was replaced with arginine (dParkin K56R), rescued pupal lethality in flies by co-expression with PINK1, whereas dParkin K77R could not. The dParkin K56R exhibited reduced abilities of mitochondrial fragmentation and motility arrest, which are mediated by degrading Parkin E3 substrates Mitofusin and Miro, respectively. Pathogenic dParkin K56N, unlike dParkin K56R, destabilized the protein, suggesting that not only was dParkin K56N non-ubiquitin-modified at K56, but also the structure of the Ubl domain for activation was largely affected. Ubiquitin attached to K27 of the Ubl domain during PINK1-mediated Parkin activation was likely to be phosphorylated because human Parkin K27R weakened Parkin self-binding and activation in trans. Therefore, our findings suggest a new mechanism of Parkin activation, where an activation complex is formed through phospho-ubiquitin attachment on the K27 residue of the Parkin Ubl domain.
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Affiliation(s)
- Jun-Yi Liu
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Tsuyoshi Inoshita
- Department of Neurodegenerative and Demented Disorders, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kahori Shiba-Fukushima
- Department of Drug Development for Parkinson’s Disease, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Shigeharu Yoshida
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yuzuru Imai
- To whom correspondence should be addressed at: Yuzuru Imai, Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan. Tel: +81 368018332; Fax: +81-3-5800-0547; ; Nobutaka Hattori, Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan, Tel: +81 358022731; Fax: +81-3-5800-0547;
| | - Nobutaka Hattori
- To whom correspondence should be addressed at: Yuzuru Imai, Research for Parkinson's Disease, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan. Tel: +81 368018332; Fax: +81-3-5800-0547; ; Nobutaka Hattori, Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan, Tel: +81 358022731; Fax: +81-3-5800-0547;
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30
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Nishida H, Ishihama Y. One-Step Isolation of Protein C-Terminal Peptides from V8 Protease-Digested Proteins by Metal Oxide-Based Ligand-Exchange Chromatography. Anal Chem 2021; 94:944-951. [PMID: 34962382 DOI: 10.1021/acs.analchem.1c03722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a one-step method to isolate protein C-terminal peptides from V8 protease-digested proteins by metal oxide-based ligand-exchange (MOLEX) chromatography. V8 protease cleaves the C-terminal side of Asp and Glu, affording a digested peptide with two carboxy groups at the C-terminus, whereas the protein C-terminal peptide has only one α-carboxy group. In MOLEX chromatography, a stable chelate is formed between dicarboxylates and metal atoms, so that the nonterminal (i.e., internal) peptide is retained, whereas the protein C-terminal peptide flows through the MOLEX column. After the optimization of the MOLEX chromatographic conditions, 1619 protein C-termini were identified from 30 μg of peptides (10 μg each, in triplicate) derived from human HeLa cells by means of nanoLC/MS/MS. When the MOLEX-isolated sample from 200 μg of HeLa peptides was further divided into six fractions by high-pH reversed-phase liquid chromatography (LC) prior to nanoLC/MS/MS, 2203 protein C-termini were identified with less than 3% contamination with internal peptides. We believe that this is the largest coverage with the highest purity reported to date in human protein C-terminomics. This fast, simple, sensitive, and selective method to isolate protein C-terminal peptides should be useful for profiling protein C-termini on a proteome-wide scale.
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Affiliation(s)
- Hiroshi Nishida
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,National Institute of Biomedical Innovation, Health and Nutrition, Laboratory of Clinical and Analytical Chemistry, Ibaraki, Osaka 567-0085, Japan
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31
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Zhang J, Uchiyama J, Imami K, Ishihama Y, Kageyama R, Kobayashi T. Novel Roles of Small Extracellular Vesicles in Regulating the Quiescence and Proliferation of Neural Stem Cells. Front Cell Dev Biol 2021; 9:762293. [PMID: 34805169 PMCID: PMC8601375 DOI: 10.3389/fcell.2021.762293] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Neural stem cell (NSC) quiescence plays pivotal roles in avoiding exhaustion of NSCs and securing sustainable neurogenesis in the adult brain. The maintenance of quiescence and transition between proliferation and quiescence are complex processes associated with multiple niche signals and environmental stimuli. Exosomes are small extracellular vesicles (sEVs) containing functional cargos such as proteins, microRNAs, and mRNAs. The role of sEVs in NSC quiescence has not been fully investigated. Here, we applied proteomics to analyze the protein cargos of sEVs derived from proliferating, quiescent, and reactivating NSCs. Our findings revealed fluctuation of expression levels and functional clusters of gene ontology annotations of differentially expressed proteins especially in protein translation and vesicular transport among three sources of exosomes. Moreover, the use of exosome inhibitors revealed exosome contribution to entrance into as well as maintenance of quiescence. Exosome inhibition delayed entrance into quiescence, induced quiescent NSCs to exit from the G0 phase of the cell cycle, and significantly upregulated protein translation in quiescent NSCs. Our results suggest that NSC exosomes are involved in attenuating protein synthesis and thereby regulating the quiescence of NSCs.
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Affiliation(s)
- Jingtian Zhang
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Junki Uchiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ryoichiro Kageyama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,RIKEN Center for Brain Science, Wako, Japan
| | - Taeko Kobayashi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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32
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Oda Y, Takahashi C, Harada S, Nakamura S, Sun D, Kiso K, Urata Y, Miyachi H, Fujiyoshi Y, Honigmann A, Uchida S, Ishihama Y, Toyoshima F. Discovery of anti-inflammatory physiological peptides that promote tissue repair by reinforcing epithelial barrier formation. Sci Adv 2021; 7:eabj6895. [PMID: 34788088 PMCID: PMC8597994 DOI: 10.1126/sciadv.abj6895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/28/2021] [Indexed: 05/10/2023]
Abstract
Epithelial barriers that prevent dehydration and pathogen invasion are established by tight junctions (TJs), and their disruption leads to various inflammatory diseases and tissue destruction. However, a therapeutic strategy to overcome TJ disruption in diseases has not been established because of the lack of clinically applicable TJ-inducing molecules. Here, we found TJ-inducing peptides (JIPs) in mice and humans that corresponded to 35 to 42 residue peptides of the C terminus of alpha 1-antitrypsin (A1AT), an acute-phase anti-inflammatory protein. JIPs were inserted into the plasma membrane of epithelial cells, which promoted TJ formation by directly activating the heterotrimeric G protein G13. In a mouse intestinal epithelial injury model established by dextran sodium sulfate, mouse or human JIP administration restored TJ integrity and strongly prevented colitis. Our study has revealed TJ-inducing anti-inflammatory physiological peptides that play a critical role in tissue repair and proposes a previously unidentified therapeutic strategy for TJ-disrupted diseases.
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Affiliation(s)
- Yukako Oda
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Chisato Takahashi
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyoto 610-0395, Japan
| | - Shota Harada
- Laboratory of Human Interface, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Shun Nakamura
- Cellular and Structural Physiology Laboratory, Advanced Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- CeSPIA Inc., Tokyo 100-0004, Japan
| | - Daxiao Sun
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01309, Germany
| | - Kazumi Kiso
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yuko Urata
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Hitoshi Miyachi
- Reproductive Engineering Team, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory, Advanced Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- CeSPIA Inc., Tokyo 100-0004, Japan
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01309, Germany
| | - Seiichi Uchida
- Laboratory of Human Interface, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Fumiko Toyoshima
- Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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33
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Niinae T, Ishihama Y, Imami K. Biotinylation-based proximity labeling proteomics: Basics, applications, and technical considerations. J Biochem 2021; 170:569-576. [PMID: 34752609 DOI: 10.1093/jb/mvab123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in biotinylation-based proximity labeling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein-protein interactions, protein-nucleic acid interactions, (membraneless) organelle proteomes, and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics, and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.
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Affiliation(s)
- Tomoya Niinae
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan
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34
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Tsumagari K, Niinae T, Otaka A, Ishihama Y. Peptide probes containing a non-hydrolyzable phosphotyrosine-mimetic residue for enrichment of protein tyrosine phosphatases. Proteomics 2021; 22:e2100144. [PMID: 34714599 DOI: 10.1002/pmic.202100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/07/2022]
Abstract
We developed peptide probes containing a non-hydrolyzable phosphotyrosine mimetic, 4-[difluoro(phosphono)methyl]-L-phenylalanine (F2 Pmp) for enrichment of protein tyrosine phosphatases (PTPs). We found that different F2 Pmp probes can enrich different PTPs, depending on the probe sequence. Furthermore, proteins containing a Src homology 2 (SH2) domain were enriched together. Importantly, probes containing phosphotyrosine instead of F2 Pmp failed to enrich PTPs due to dephosphorylation during the pulldown step. This enrichment approach using peptides containing F2 Pmp could be a generic tool for tyrosine phosphatome analysis without the use of antibodies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kazuya Tsumagari
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.,Center for Integrated Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Tokushima, 770-8505, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan
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35
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Akaki K, Ogata K, Yamauchi Y, Iwai N, Tse KM, Hia F, Mochizuki A, Ishihama Y, Mino T, Takeuchi O. IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay. eLife 2021; 10:71966. [PMID: 34636324 PMCID: PMC8553338 DOI: 10.7554/elife.71966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/08/2021] [Indexed: 01/14/2023] Open
Abstract
Regnase-1 is an endoribonuclease crucial for controlling inflammation by degrading mRNAs encoding cytokines and inflammatory mediators in mammals. However, it is unclear how Regnase-1-mediated mRNA decay is controlled in interleukin (IL)-1β- or Toll-like receptor (TLR) ligand-stimulated cells. Here, by analyzing the Regnase-1 interactome, we found that IL-1β or TLR stimulus dynamically induced the formation of Regnase-1-β-transducin repeat-containing protein (βTRCP) complex. Importantly, we also uncovered a novel interaction between Regnase-1 and 14-3-3 in both mouse and human cells. In IL-1R/TLR-stimulated cells, the Regnase-1-14-3-3 interaction is mediated by IRAK1 through a previously uncharacterized C-terminal structural domain. Phosphorylation of Regnase-1 at S494 and S513 is critical for Regnase-1-14-3-3 interaction, while a different set of phosphorylation sites of Regnase-1 is known to be required for the recognition by βTRCP and proteasome-mediated degradation. We found that Regnase-1-14-3-3 and Regnase-1-βTRCP interactions are not sequential events. Rather, 14-3-3 protects Regnase-1 from βTRCP-mediated degradation. On the other hand, 14-3-3 abolishes Regnase-1-mediated mRNA decay by inhibiting Regnase-1-mRNA association. In addition, nuclear-cytoplasmic shuttling of Regnase-1 is abrogated by 14-3-3 interaction. Taken together, the results suggest that a novel inflammation-induced interaction of 14-3-3 with Regnase-1 stabilizes inflammatory mRNAs by sequestering Regnase-1 in the cytoplasm to prevent mRNA recognition.
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Affiliation(s)
- Kotaro Akaki
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuhei Yamauchi
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ka Man Tse
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Mochizuki
- Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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36
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Ichihara K, Matsumoto A, Nishida H, Kito Y, Shimizu H, Shichino Y, Iwasaki S, Imami K, Ishihama Y, Nakayama KI. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons. Nucleic Acids Res 2021; 49:7298-7317. [PMID: 34226921 PMCID: PMC8287933 DOI: 10.1093/nar/gkab549] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/05/2023] Open
Abstract
Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here, we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are most probably dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
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Affiliation(s)
- Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hiroshi Nishida
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Kito
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan
| | - Koshi Imami
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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37
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Abstract
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chia-Feng Tsai
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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38
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Matsumoto A, Takahashi Y, Ogata K, Kitamura S, Nakagawa N, Yamamoto A, Ishihama Y, Takakura Y. Phosphatidylserine-deficient small extracellular vesicle is a major somatic cell-derived sEV subpopulation in blood. iScience 2021; 24:102839. [PMID: 34368655 PMCID: PMC8326202 DOI: 10.1016/j.isci.2021.102839] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/09/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022] Open
Abstract
Small extracellular vesicles (sEVs) are important mediators of intercellular communication with respect to diverse pathophysiological processes. Here, we determined novel phosphatidylserine (PS)-deficient sEV subpopulations as a major somatic cell-derived sEV subpopulation in blood because of long blood circulation half-life through escape from macrophage uptake. PS(-)-sEVs were identified in various cultured cells as a minor population. However, as a result of rapid uptake of PS(+)-sEVs by macrophages, circulating somatic cell-derived sEVs in the blood were found to be mainly PS(-)-sEVs. These results suggest that endogenous PS(-)-sEVs could indeed be the key player in sEV-mediated intercellular communication, a good target for sEV-based diagnosis, and a potent candidate for sEV-based drug delivery. Our findings bring a paradigm shift in the understanding of the biology and translational applications of sEVs.
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Affiliation(s)
- Akihiro Matsumoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Shimpei Kitamura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoki Nakagawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aki Yamamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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39
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Uchiyama J, Ishihama Y, Imami K. Quantitative nascent proteome profiling by dual-pulse labelling with O-propargyl-puromycin and stable isotope-labelled amino acids. J Biochem 2021; 169:227-236. [PMID: 32926143 DOI: 10.1093/jb/mvaa104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/30/2020] [Indexed: 11/13/2022] Open
Abstract
Monitoring translational regulation in response to environmental signals is crucial for understanding cellular proteostasis. However, only limited approaches are currently available for quantifying acute changes in protein synthesis induced by stimuli. Recently, a clickable puromycin analogue, O-propargyl-puromycin (OPP), was developed and applied to label the C-termini of nascent polypeptide chains (NPCs). Following affinity purification via a click reaction, OPP allows for a proteomic analysis of NPCs. Despite its advantage, the affinity purification of NPCs using magnetic beads or resins inherently suffers from significant non-specific protein binding, which hinders accurate quantification of the nascent proteins. To address this issue, we employed dual-pulse labelling of NPCs with both OPP and stable isotope-labelled amino acids to distinguish bona fide NPCs from non-specific proteins, thereby enabling the accurate quantitative profiling of NPCs. We applied this method to dissecting translation responses upon transcriptional inhibition and quantified ∼3,000 nascent proteins. We found that the translation of a subset of ribosomal proteins (e.g. RPSA, RPLP0) as well as signalling proteins (e.g. BCAR3, EFNA1, DUSP1) was significantly repressed by transcription inhibition. Together, the present method provides an accurate and broadly applicable nascent proteome profiling for many biological applications at the level of translation.
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Affiliation(s)
- Junki Uchiyama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Department of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo 102-0075, Japan
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40
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Niinae T, Imami K, Sugiyama N, Ishihama Y. Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs. Mol Cell Proteomics 2021; 20:100119. [PMID: 34186244 PMCID: PMC8325102 DOI: 10.1016/j.mcpro.2021.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass-spectrometry-based phosphoproteomics can identify more than 10,000 phosphorylated sites in a single experiment. But, despite the fact that enormous phosphosite information has been accumulated in public repositories, protein kinase–substrate relationships remain largely unknown. Here, we describe a method to identify endogenous substrates of kinases by using a combination of a proximity-dependent biotin identification method, called BioID, with two other independent methods, kinase-perturbed phosphoproteomics and phosphorylation motif matching. For proof of concept, this approach was applied to casein kinase 2 (CK2) and protein kinase A (PKA), and we identified 24 and 35 putative substrates, respectively. We also show that known cancer-associated missense mutations near phosphosites of substrates affect phosphorylation by CK2 or PKA and thus might alter downstream signaling in cancer cells bearing these mutations. This approach extends our ability to probe physiological kinase–substrate networks by providing new methodology for large-scale identification of endogenous substrates of kinases. Identification of novel kinase interactors by BioID. Applying two orthogonal filters, kinase perturbation and phosphorylation motif. Identification of novel CK2 and PKA substrates. A universal method for the identification of endogenous substrates for all kinases.
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Affiliation(s)
- Tomoya Niinae
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Koshi Imami
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; PRESTO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
| | - Naoyuki Sugiyama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.
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41
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Chang CH, Yeung D, Spicer V, Ogata K, Krokhin O, Ishihama Y. Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry. J Proteome Res 2021; 20:3600-3610. [PMID: 34133192 DOI: 10.1021/acs.jproteome.1c00185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The contribution of peptide amino acid sequence to collision cross section values (CCS) has been investigated using a dataset of ∼134 000 peptides of four different charge states (1+ to 4+). The migration data were acquired using a two-dimensional liquid chromatography (LC)/trapped ion mobility spectrometry/quadrupole/time-of-flight mass spectrometry (MS) analysis of HeLa cell digests created using seven different proteases and was converted to CCS values. Following the previously reported modeling approaches using intrinsic size parameters (ISP), we extended this methodology to encode the position of individual residues within a peptide sequence. A generalized prediction model was built by dividing the dataset into eight groups (four charges for both tryptic/nontryptic peptides). Position-dependent ISPs were independently optimized for the eight subsets of peptides, resulting in prediction accuracy of ∼0.981 for the entire population of peptides. We find that ion mobility is strongly affected by the peptide's ability to solvate the positively charged sites. Internal positioning of polar residues and proline leads to decreased CCS values as they improve charge solvation; conversely, this ability decreases with increasing peptide charge due to electrostatic repulsion. Furthermore, higher helical propensity and peptide hydrophobicity result in a preferential formation of extended structures with higher than predicted CCS values. Finally, acidic/basic residues exhibit position-dependent ISP behavior consistent with electrostatic interaction with the peptide macrodipole, which affects the peptide helicity. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (http://jpostdb.org) with the dataset identifiers PXD021440/JPST000959, PXD022800/JPST001017, and PXD026087/ JPST001176.
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Affiliation(s)
- Chih-Hsiang Chang
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Oleg Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg, Manitoba R3T 2N2, Canada
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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42
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Tsumagari K, Ishihama Y. Acylated peptide enrichment utilizing lysine deacylases for lysine acylomics. Biochem Biophys Res Commun 2021; 563:60-65. [PMID: 34062387 DOI: 10.1016/j.bbrc.2021.05.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 01/22/2023]
Abstract
Reversible acylation of lysine ε-amino groups, e.g., acetylation, succinylation, maronylation, and myristoylation, is involved in basic physiological processes such as metabolism, cell signaling and aging. In this study, we developed a novel enrichment method for acylated peptides without the use of antibodies, in which endogenously acylated peptides are deacylated by recombinant lysine deacylases based on the enzyme-substrate relationship and enriched by N-hydroxysuccinimidyl chemistry for identification of the acylated sites by nanoscale liquid chromatography-tandem mass spectrometric analysis. To demonstrate the validity of this acylomics platform, we used it to identify acylated sites on chemically acylated model protein samples. We also applied it to the nuclei of HeLa cells to identify endogenous acylated sites.
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Affiliation(s)
- Kazuya Tsumagari
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan; Eisai-Keio Innovation Laboratory for Dementia, Center for Integrated Medical Research, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan; Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
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43
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Yokoyama T, Niinae T, Tsumagari K, Imami K, Ishihama Y, Hizukuri Y, Akiyama Y. The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J Biol Chem 2021; 296:100673. [PMID: 33865858 PMCID: PMC8144685 DOI: 10.1016/j.jbc.2021.100673] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli RseP, a member of the site-2 protease family of intramembrane proteases, is involved in the activation of the σE extracytoplasmic stress response and elimination of signal peptides from the cytoplasmic membrane. However, whether RseP has additional cellular functions is unclear. In this study, we used mass spectrometry-based quantitative proteomic analysis to search for new substrates that might reveal unknown physiological roles for RseP. Our data showed that the levels of several Fec system proteins encoded by the fecABCDE operon (fec operon) were significantly decreased in an RseP-deficient strain. The Fec system is responsible for the uptake of ferric citrate, and the transcription of the fec operon is controlled by FecI, an alternative sigma factor, and its regulator FecR, a single-pass transmembrane protein. Assays with a fec operon expression reporter demonstrated that the proteolytic activity of RseP is essential for the ferric citrate-dependent upregulation of the fec operon. Analysis using the FecR protein and FecR-derived model proteins showed that FecR undergoes sequential processing at the membrane and that RseP participates in the last step of this sequential processing to generate the N-terminal cytoplasmic fragment of FecR that participates in the transcription of the fec operon with FecI. A shortened FecR construct was not dependent on RseP for activation, confirming this cleavage step is the essential and sufficient role of RseP. Our study unveiled that E. coli RseP performs the intramembrane proteolysis of FecR, a novel physiological role that is essential for regulating iron uptake by the ferric citrate transport system.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuya Tsumagari
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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44
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Yuizumi N, Harada Y, Kuniya T, Sunabori T, Koike M, Wakabayashi M, Ishihama Y, Suzuki Y, Kawaguchi D, Gotoh Y. Maintenance of neural stem-progenitor cells by the lysosomal biosynthesis regulators TFEB and TFE3 in the embryonic mouse telencephalon. Stem Cells 2021; 39:929-944. [PMID: 33609411 DOI: 10.1002/stem.3359] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/26/2021] [Indexed: 11/09/2022]
Abstract
Lysosomes have recently been implicated in regulation of quiescence in adult neural stem cells (NSCs). Whether lysosomes regulate the differentiation of neural stem-progenitor cells (NPCs) in the embryonic brain has remained unknown, however. We here show that lysosomes are more abundant in rapidly dividing NPCs than in differentiating neurons in the embryonic mouse neocortex and ganglionic eminence. The genes for TFEB and TFE3, master regulators of lysosomal biosynthesis, as well as other lysosome-related genes were also expressed at higher levels in NPCs than in differentiating neurons. Anatomic analysis revealed accumulation of lysosomes at the apical and basal endfeet of NPCs. Knockdown of TFEB and TFE3, or that of the lysosomal transporter Slc15a4, resulted in premature differentiation of neocortical NPCs. Conversely, forced expression of an active form of TFEB (TFEB-AA) suppressed neuronal differentiation of NPCs in association with upregulation of NPC-related genes. These results together point to a previously unappreciated role for TFEB and TFE3, and possibly for lysosomes, in maintenance of the undifferentiated state of embryonic NPCs. We further found that lysosomes are even more abundant in an NPC subpopulation that rarely divides and includes the embryonic origin of adult NSCs than in the majority of NPCs that divide frequently for construction of the embryonic brain, and that overexpression of TFEB-AA also suppressed the cell cycle of neocortical NPCs. Our results thus also implicate lysosomes in establishment of the slowly dividing, embryonic origin of adult NSCs.
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Affiliation(s)
- Naoya Yuizumi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yujin Harada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takaaki Kuniya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Sunabori
- Department of Cell Biology and Neuroscience, Juntendo University of Medicine, Tokyo, Japan
| | - Masato Koike
- Department of Cell Biology and Neuroscience, Juntendo University of Medicine, Tokyo, Japan
| | - Masaki Wakabayashi
- Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Daichi Kawaguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
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45
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Taechawattananant P, Yoshii K, Ishihama Y. Peak Identification and Quantification by Proteomic Mass Spectrogram Decomposition. J Proteome Res 2021; 20:2291-2298. [PMID: 33661642 DOI: 10.1021/acs.jproteome.0c00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent advances in the liquid chromatography/mass spectrometry (LC/MS) technology have improved the sensitivity, resolution, and speed of proteome analysis, resulting in increasing demand for more sophisticated algorithms to interpret complex mass spectrograms. Here, we propose a novel statistical method, proteomic mass spectrogram decomposition (ProtMSD), for joint identification and quantification of peptides and proteins. Given the proteomic mass spectrogram and the reference mass spectra of all possible peptide ions associated with proteins as a dictionary, ProtMSD estimates the chromatograms of those peptide ions under a group sparsity constraint without using the conventional careful preprocessing (e.g., thresholding and peak picking). We show that the method was significantly improved using protein-peptide hierarchical relationships, isotopic distribution profiles, reference retention times of peptide ions, and prelearned mass spectra of noise. We examined the concept of database search, library search, and match-between-runs. Our ProtMSD showed excellent agreements of 3277 peptide ions (94.79%) and 493 proteins (98.21%) with Mascot/Skyline for an Escherichia coli proteome sample and of 4460 peptide ions (103%) and 588 proteins (101%) with match-between-runs by MaxQuant for a yeast proteome sample. This is the first attempt to use a matrix decomposition technique as a tool for LC/MS-based proteome identification and quantification.
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Affiliation(s)
| | - Kazuyoshi Yoshii
- Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan.,RIKEN Center for Advanced Intelligence Project (AIP), Tokyo 103-0027, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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46
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Tsumagari K, Chang CH, Ishihama Y. Exploring the landscape of ectodomain shedding by quantitative protein terminomics. iScience 2021; 24:102259. [PMID: 33796845 PMCID: PMC7995609 DOI: 10.1016/j.isci.2021.102259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/18/2021] [Accepted: 02/26/2021] [Indexed: 02/08/2023] Open
Abstract
Ectodomain shedding is a proteolytic process that regulates the levels and functions of membrane proteins. Dysregulated shedding is linked to severe diseases, including cancer and Alzheimer's disease. However, the exact cleavage sites of shedding substrates remain largely unknown. Here, we explore the landscape of ectodomain shedding by generating large-scale, cell-type-specific maps of shedding cleavage sites. By means of N- and C-terminal peptide enrichment and quantitative mass spectrometry, we quantified protein termini in the culture media of 10 human cell lines and identified 489 cleavage sites on 163 membrane proteins whose proteolytic terminal fragments are downregulated in the presence of a broad-spectrum metalloprotease inhibitor. A major fraction of the presented cleavage sites was identified in a cell-type-specific manner and mapped onto receptors, cell adhesion molecules, and protein kinases and phosphatases. We confidently identified 86 cleavage sites as metalloprotease substrates by means of knowledge-based scoring. Secretomes across 10 human cell lines were investigated by protein terminomics Cell-type-specific maps of shedding cleavage sites were generated Most of the cleavage sites were identified in a cell-type-specific manner Knowledge-based scoring enabled prediction of responsible sheddases
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Affiliation(s)
- Kazuya Tsumagari
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Eisai-Keio Innovation Laboratory for Dementia, Center for Integrated Medical Research, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Chih-Hsiang Chang
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Department of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Corresponding author
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47
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Ogata K, Chang CH, Ishihama Y. Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry. Mass Spectrom (Tokyo) 2021; 10:A0093. [PMID: 33552826 PMCID: PMC7843839 DOI: 10.5702/massspectrometry.a0093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
The insertion of ion mobility spectrometry (IMS) between LC and MS can improve peptide identification in both proteomics and phosphoproteomics by providing structural information that is complementary to LC and MS, because IMS separates ions on the basis of differences in their shapes and charge states. However, it is necessary to know how phosphate groups affect the peptide collision cross sections (CCS) in order to accurately predict phosphopeptide CCS values and to maximize the usefulness of IMS. In this work, we systematically characterized the CCS values of 4,433 pairs of mono-phosphopeptide and corresponding unphosphorylated peptide ions using trapped ion mobility spectrometry (TIMS). Nearly one-third of the mono-phosphopeptide ions evaluated here showed smaller CCS values than their unphosphorylated counterparts, even though phosphorylation results in a mass increase of 80 Da. Significant changes of CCS upon phosphorylation occurred mainly in structurally extended peptides with large numbers of basic groups, possibly reflecting intramolecular interactions between phosphate and basic groups.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Chih-Hsiang Chang
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606–8501, Japan
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48
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Watanabe Y, Aoki-Kinoshita KF, Ishihama Y, Okuda S. GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Nucleic Acids Res 2021; 49:D1523-D1528. [PMID: 33174597 PMCID: PMC7778884 DOI: 10.1093/nar/gkaa1012] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
For the reproducibility and sustainability of scientific research, FAIRness (Findable, Accessible, Interoperable and Re-usable), with respect to the release of raw data obtained by researchers, is one of the most important principles underpinning the future of open science. In genomics and transcriptomics, the sharing of raw data from next-generation sequencers is made possible through public repositories. In addition, in proteomics, the deposition of raw data from mass spectrometry (MS) experiments into repositories is becoming standardized. However, a standard repository for such MS data had not yet been established in glycomics. With the increasing number of glycomics MS data, therefore, we have developed GlycoPOST (https://glycopost.glycosmos.org/), a repository for raw MS data generated from glycomics experiments. In just the first year since the release of GlycoPOST, 73 projects have already been registered by researchers around the world, and the number of registered projects is continuously growing, making a significant contribution to the future FAIRness of the glycomics field. GlycoPOST is a free resource to the community and accepts (and will continue to accept in the future) raw data regardless of vendor-specific formats.
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Affiliation(s)
- Yu Watanabe
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Kiyoko F Aoki-Kinoshita
- Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.,Department of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
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49
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Ishihama Y, Chen YJ, Cho JY, Ming Chung MC, Cordwell SJ, Low TY, Wai Poon TC, Kwon HJ. Asia-Oceania HUPO: Past, Present, and Future. Mol Cell Proteomics 2021; 20:100048. [PMID: 33465491 PMCID: PMC7950209 DOI: 10.1016/j.mcpro.2021.100048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022] Open
Abstract
The Asia-Oceania Human Proteome Organization (AOHUPO; www.aohupo.org) was officially founded on June 7, 2001, by Richard J. Simpson (Australia), Akira Tsugita (Japan), and Young-Ki Paik (Korea) and launched on October 1-4, 2001, at the second scientific meeting of the International Proteomics Conference held in Canberra, Australia. Inaugural council members of the AOHUPO elected were Richard J. Simpson (Australia, president), Qi-Chang Xia (China), Kazuyuki Nakamura (Japan), Akira Tsugita (Japan, VIce President), Young-Ki Paik (Korea, secretary general), Mike Hubbard (New Zealand), Max C. M. Chung (Singapore), Shui-Tien Chen (Taiwan), and John Bennett (Philippines). The first AOHUPO conference was held on March 26-27, 2002, at the Seoul National University, Seoul, Korea, conjointly with the second Annual Meeting of KHUPO. Since then, biennial AOHUPO conferences have been held in Taipei (2004), Singapore (2006), Cairns (2008), Hyderabad (2010), Beijing (2012), Bangkok (2014), Sun Moon Lake (2016), and Osaka (2018). The 10th AOHUPO conference is scheduled to be held in Busan on June 30 to July 2, 2021, to celebrate our 20th anniversary.
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Affiliation(s)
- Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Max Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Stuart J Cordwell
- School of Life and Environmental Sciences and Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Terence Chuen Wai Poon
- Pilot Laboratory, Proteomics Core, Institute of Translational Medicine, Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Ho Jeong Kwon
- Chemical Genomics GRL, Department of Biotechnology, Yonsei University, Seoul, South Korea
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50
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Oka M, Xu L, Suzuki T, Yoshikawa T, Sakamoto H, Uemura H, Yoshizawa AC, Suzuki Y, Nakatsura T, Ishihama Y, Suzuki A, Seki M. Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. Genome Biol 2021; 22:9. [PMID: 33397462 PMCID: PMC7780684 DOI: 10.1186/s13059-020-02240-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified. RESULTS Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection. CONCLUSIONS Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.
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Affiliation(s)
- Miho Oka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Ono Pharmaceutical Co., Ltd., Ibaraki, Japan
| | - Liu Xu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toshihiro Suzuki
- General Medical Education and Research Center, Teikyo University, Tokyo, Japan
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Toshiaki Yoshikawa
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hiromi Sakamoto
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hayato Uemura
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akiyasu C. Yoshizawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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