Metabolomics of small extracellular vesicles derived from isocitrate dehydrogenase 1-mutant HCT116 cells collected by semi-automated size exclusion chromatography

Ryosuke Hayasaka; Sho Tabata; Masako Hasebe; Satsuki Ikeda; Tomoya Hikita; Chitose Oneyama; Jun Yoshitake; Daisuke Onoshima; Kumiko Takahashi; Takahiro Shibata; Koji Uchida; Yoshinobu Baba; Tomoyoshi Soga; Masaru Tomita; Akiyoshi Hirayama

doi:10.3389/fmolb.2022.1049402

Metabolomics of small extracellular vesicles derived from isocitrate dehydrogenase 1-mutant HCT116 cells collected by semi-automated size exclusion chromatography

Front Mol Biosci. 2023 Jan 11:9:1049402. doi: 10.3389/fmolb.2022.1049402. eCollection 2022.

Authors

Ryosuke Hayasaka^{1

2}, Sho Tabata³, Masako Hasebe¹, Satsuki Ikeda¹, Tomoya Hikita⁴, Chitose Oneyama^{4

5

6

7}, Jun Yoshitake⁷, Daisuke Onoshima⁷, Kumiko Takahashi⁸, Takahiro Shibata⁹, Koji Uchida^{10

11}, Yoshinobu Baba^{7

12

13

14}, Tomoyoshi Soga^{1

2}, Masaru Tomita^{1

2}, Akiyoshi Hirayama^{1

2

7}

Affiliations

¹ Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
² Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
³ Institute for Protein Research, Osaka University, Suita, Japan.
⁴ Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, Nagoya, Japan.
⁵ Department of Oncology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.
⁶ Department of Target and Drug Discovery, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
⁷ Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan.
⁸ Materials Integration Laboratories, AGC Inc., Yokohama, Japan.
⁹ Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
¹⁰ Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
¹¹ Japan Agency for Medical Research and Development, CREST, Tokyo, Japan.
¹² Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
¹³ Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan.
¹⁴ College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.

Abstract

Cancer-derived small extracellular vesicles (sEVs) are multifunctional particles with a lipid bilayer structure that are involved in cancer progression, such as malignant proliferation, distant metastasis, and cancer immunity evasion. The separation protocol used to isolate sEVs is an important process and thus, several have been developed, including ultracentrifugation (UC), size exclusion chromatography (SEC), and affinity purification using antibodies against sEV surface antigens. However, the effects of different separation methods on sEV components have not been adequately examined. Here, we developed a semi-automated system for collecting sEVs by combining SEC and preparative high-performance liquid chromatography and applied it to metabolome analysis. The developed SEC system could recover sEVs more efficiently and non-destructively than UC, suggesting that it is an appropriate recovery method for metabolic analysis and reflects biological conditions. Furthermore, using the developed SEC system, we performed metabolome analysis of sEVs from isocitrate dehydrogenase 1 (IDH)-mutated human colon HCT116 cells, which produce the oncogenic metabolite, 2-hydroxyglutaric acid (2-HG). IDH1-mutated HCT116 cells released significantly more sEVs than wild-type (WT) cells. The metabolomic profiles of IDH1 mutant and WT cells showed distinct differences between the cells and their sEVs. Notably, in IDH mutant cells, large amounts of 2-HG were detected not only in cells, but also in sEVs. These results indicate that the SEC system we developed has wide potential applications in sEVs research.

Keywords: 2-hydroxyglutaric acid; lipidome analysis; metabolome analysis; oncometabolites; size exclusion chromatography; small extracellular vesicles; ultracentrifugation.

Grants and funding

This research was supported in part by JSPS KAKENHI grant numbers JP20J12816 (RH), JP18H04804 (AH), and JP18K08219 (AH); the Japan Agency for Medical Research and Development, AMED grant number JP18dk0207043 (AH); Taikichiro Mori Memorial Research Grants (RH); the Center of Innovation Program at Nagoya University (Nagoya University–COI) from the Japan Science and Technology Agency (JST); and grants from the Yamagata Prefectural Government and the city of Tsuruoka.