In-depth quantitative analysis and comparison of the human hepatocyte and hepatoma cell line HepG2 proteomes
Open accessAbstract
Hepatocytes play a pivotal role in human homeostasis. They are essential in regulation of glucose and lipid levels in blood and play a central role in metabolism of amino acids, lipids, drugs and xenobiotic-compounds. In addition, hepatocytes produce a major portion of proteins circulating in the blood. Hepatocytes were isolated from liver tissue obtained from surgical resections. Proteins were extracted and processed using filter aided sample preparation protocol and were analyzed by LC-MS/MS using high accuracy mass spectrometry. Proteins were quantified by the 'Total Protein Approach' and 'Proteomic Ruler'. We report a comprehensive proteomic analysis of purified human hepatocytes and the human hepatoma cell line HepG2. The complete dataset comprises 9400 proteins and provides a comprehensive and quantitative depiction of the proteomes of hepatocytes and HepG2 cells at the protein titer and copy number dimensions. We describe basic cell organization and in detail energy metabolism pathways and metabolite transport. We provide quantitative insights into protein synthesis and drug and xenobiotics catabolism. Our data delineate differences between the native human hepatocytes and HepG2 cells by providing for the first time quantitative data at protein concentrations and copy numbers.
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The measured STAT3 protein concentration in primary mouse hepatocytes is in good agreement with published data from primary human hepatocytes.
“The obtained value for STAT3 is in good agreement with recently published data from a mass spectrometry approach to determine molecules per cell in primary human hepatocytes (Wisniewski et al., 2016).”
From Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib (2017) · cites this paper as Wisniewski et al., 2016
Section 3.3 describes mass-spectrometry-based estimates of protein copies per cell in human hepatocytes, supporting the description of the cited dataset. The passages found do not give a STAT3 value or establish that it agrees with the citing paper’s mouse-hepatocyte measurement (searched: STAT3 and its full protein name). (LLM, conf=0.78)
Experimental — accuracy not yet measuredHep G2 cells' oxygen consumption rate per tissue volume, 4 × 10-17 mol cell-1 s-1 at an estimated compact cell density of 1.1 × 109 cm-3 yielding 4 × 10-8 mol cm-3 s-1, is a good approximation of human liver tissue.
“Hep G2 cells were used in this part of the study, since their oxygen consumption rate per tissue volume, 4 × 10 -17 mol cell -1 s -1 [29] at an estimated compact cell density of 1.1 × 10 9 cm -3 (cell volume of 850 μm 3 [30] ) yielding 4 × 10 -8 mol cm -3 s -1 , is a good approximation of human liver tissue.”
From 3D microperfusion of mesoscale human microphysiological liver models improves functionality and recapitulates hepatic zonation (2023) · cites this paper as [30]
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Cites
Godoy, P., Hewitt, N. J., Albrecht, U., Andersen, M. E., Ansari, N., Bhattacharya, S., Bode, J. G., Bolleyn, J., Borner, C., Böttger, J., et al. (2013) · Archives of Toxicology · doi:10.1007/s00204-013-1078-5 · Cited by 1,280 · see citing works
A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
Wiśniewski, J. R., Hein, M. Y., Cox, J., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.037309 · Cited by 690 · see citing works
Self-citationWiśniewski, J. R., Zougman, A., & Mann, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900748n · Cited by 545 · see citing works
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Research works printed but not linked: 4
- M.N. Berry, Edwards AM, The Hepatocyte Review, Kulwer Academic Publishers, 2000.
- I. Brockhausen, H. Schachter, P. Stanley, O-GalNAc Glycans, in: A. Varki, Cummings RD, Esko JD, Freeze HH, P. Stanley, Bertozzi CR, et al., (Eds.), Essentials of Glycobiology, second ed.Cold Spring Harbor, NY, 2009.
- P. Stanley, H. Schachter, N. Taniguchi, N-Glycans, in: A. Varki, Cummings RD, Esko JD, Freeze HH, P. Stanley, Bertozzi CR, et al., (Eds.), Essentials of Glycobiology, second ed.Cold Spring Harbor, NY, 2009.
- A. Varki, R. Schauer, Sialic Acids, in: A. Varki, Cummings RD, Esko JD, Freeze HH, P. Stanley, Bertozzi CR, et al. (Eds.), Essentials of Glycobiology, second ed.Cold Spring Harbor, NY, 2009.
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Liu, X., Fang, J., Huang, S., Wu, X., Xie, X., Wang, J., Liu, F., Zhang, M., Peng, Z., & Hu, N. (2021) · Microsystems & Nanoengineering · doi:10.1038/s41378-021-00277-8 · Cited by 246 · see citing works
Structural basis for species-selective targeting of Hsp90 in a pathogenic fungus
Whitesell, L., Robbins, N., Huang, D. S., McLellan, C. A., Shekhar-Guturja, T., LeBlanc, E. V., Nation, C. S., Hui, R., Hutchinson, A., Collins, C., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08248-w · Cited by 124 · see citing works
Precision-cut human liver slice cultures as an immunological platform
Wu, X., Roberto, J. B., Knupp, A., Kenerson, H. L., Truong, C. D., Yuen, S. Y., Brempelis, K. J., Tuefferd, M., Chen, A., Horton, H., et al. (2018) · Journal of Immunological Methods · doi:10.1016/j.jim.2018.01.012 · Cited by 81 · see citing works
Wesseler, M. F., Taebnia, N., Harrison, S., Youhanna, S., Preiss, L. C., Kemas, A. M., Vegvari, A., Mokry, J., Sullivan, G. J., Lauschke, V. M., et al. (2023) · Acta Biomaterialia · doi:10.1016/j.actbio.2023.09.022 · Cited by 39 · see citing works
Sobotta, S., Raue, A., Huang, X., Vanlier, J., Jünger, A., Bohl, S., Albrecht, U., Hahnel, M. J., Wolf, S., Mueller, N. S., et al. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00775 · Cited by 28 · see citing works
“The obtained value for STAT3 is in good agreement with recently published data from a mass spectrometry approach to determine molecules per cell in primary human hepatocytes (Wisniewski et al., 2016).”
Result
- Authors
- Wiśniewski, J. R., Vildhede, A., Norén, A., & Artursson, P.
- Affiliations
- Max Planck Institute of Biochemistry (DE)
- Uppsala University (SE)
- Corresponding author
- Wiśniewski, Jacek R.
- Venue
- Journal of Proteomics
- Publisher
- Elsevier BV
- Published
- 2016-03
- Volume
- 136
- Pages
- 234-247
- ISSN
- 1874-3919 (ISSN-L)
- OpenAlex
- W2252267431
- Cited by
- 185
- References
- 3
- Citations by year
- 2026: 10 · 2025: 24 · 2024: 14 · 2023: 16 · 2022: 18 · 2021: 16 · 2020: 18 · 2019: 23 · 2018: 16 · 2017: 19 · 2016: 10
- FWCI
- 11.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Proteomics (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion, other-oa)
- Funders
- Vetenskapsrådet
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- human hepatocytes, HepG2 cells, hepatoma cell lines, quantitative proteomics, protein copy number, energy metabolism, metabolite transport, drug metabolism, protein synthesis, liver
- MeSH terms
- Carcinoma, Hepatocellular, Humans, Liver Neoplasms, Neoplasm Proteins, Hepatocytes, Hep G2 Cells
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