Comparison of protein expression between human livers and the hepatic cell lines HepG2, Hep3B,and Huh7 using SWATH and MRM-HR proteomics: Focusing on drug-metabolizing enzymes |
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| Institution: | 1. Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States;2. Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, United States;3. Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, United States;3. From the Departments of Microbiology and Immunology, Medical University of South Carolina, Charleston South Carolina 29425;4. Departments of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston South Carolina 29425;6. Department of Public Health, Medical University of South Carolina, Charleston South Carolina 29425;5. the Department of Molecular Biology and Genetics, 34662 Istanbul, Turkey;1. BK21 Plus KNU Multi-Omics-based Creative Drug Research Team, College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea;2. BK21 PLUS Team for Creative Leader Program for Pharmacomics-based Future Pharmacy and Integrated Research Institute of Pharmaceutical Sciences, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea;3. Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Republic of Korea;1. Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, 14152 Stockholm, Sweden;2. Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden;3. Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden;4. Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA;5. Public Health Agency of Sweden, Solna, Sweden;6. Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden;1. Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku Kawasaki-shi, Kanagawa, 210-9501, Japan;2. Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura City, Kanagawa, 247-8530, Japan;3. Astellas Pharma Inc., 21 Miyukigaoka, Tsukubashi, Ibaraki, 305-8585, Japan;4. Sumitomo Dainippon Pharma Co., Ltd, 33-94 Enokicho, Suita-shi, Osaka, 554-0022, Japan;5. Sumitomo Dainippon Pharma Co., Ltd, 1-13-1 Kyobashi, Chuo-ku, Tokyo, 104-8356, Japan;6. CMIC Pharma Science Co., Ltd, Formerly JCL Bioassay Corporation, 17-18, Nakahata-cho, Nishiwaki-shi, Hyogo, 677-0032, Japan;7. Kyowa Hakko Kirin Co., Ltd, 1188, Shimotogari, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-9731, Japan;8. LSI Medience Corporation, 30-1, Shimura 3-chome, Itabashi-ku, Tokyo, 174-8555, Japan;9. LSI Medience Corporation, 14-1 Sunayama, Kamisu, Ibaraki, 314-0255, Japan;10. LSI Medience Corporation, 1285 Kurisaki-machi, Uto, Kumamoto, 869-0425, Japan;11. Shin Nippon Biomedicals Laboratories, Ltd, 2438 Miyanoura, Kagoshima, 891-1394, Japan;12. Sumika Chemical Analysis Service, Ltd, 3-1-135 Kasugadenaka, Konohana-ku, Osaka, 554-0022, Japan;13. Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan;1. Laboratory Animal Research Department, Japan;2. Pathology Analysis Center, Japan;3. ICLAS Monitoring Center, Central Institute for Experimental Animals, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan;4. ADME & Tox. Research Institute, Sekisui Medical Co., Ltd., 3-13-5 Nihombashi, Chuo-ku, Tokyo, 103-0027, Japan;5. Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan;6. Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, 683-8503, Japan;7. Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo, 194-8543, Japan;8. Department of Gastroenterology and Hepatology, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan |
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| Abstract: | Human hepatic cell lines are widely used as an in vitro model for the study of drug metabolism and liver toxicity. However, the validity of this model is still a subject of debate because the expressions of various proteins in the cell lines, including drug-metabolizing enzymes (DMEs), can differ significantly from those in human livers. In the present study, we first conducted an untargeted proteomics analysis of the microsomes of the cell lines HepG2, Hep3B, and Huh7, and compared them to human livers using a sequential window acquisition of all theoretical mass spectra (SWATH) method. Furthermore, high-resolution multiple reaction monitoring (MRM-HR), a targeted proteomic approach, was utilized to compare the expressions of pre-selected DMEs between human livers and the cell lines. In general, the SWATH quantifications were in good agreement with the MRM-HR analysis. Over 3000 protein groups were quantified in the cells and human livers, and the proteome profiles of human livers significantly differed from the cell lines. Among the 101 DMEs quantified with MRM-HR, most were expressed at substantially lower levels in the cell lines. Thus, appropriate caution must be exercised when using these cell lines for the study of hepatic drug metabolism and toxicity. |
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| Keywords: | Drug-metabolizing enzymes Hep3B HepG2 Huh7 Human livers MRM-HR SWATH |
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