Proteomic profiling of murine biliary-derived hepatic organoids and their capacity for drug disposition, bioactivation and detoxification
Open accessAbstract
Hepatic organoids are a recent innovation in in vitro modeling. Initial studies suggest that organoids better recapitulate the liver phenotype in vitro compared to pre-existing proliferative cell models. However, their potential for drug metabolism and detoxification remains poorly characterized, and their global proteome has yet to be compared to their tissue of origin. This analysis is urgently needed to determine what gain-of-function this new model may represent for modeling the physiological and toxicological response of the liver to xenobiotics. Global proteomic profiling of undifferentiated and differentiated hepatic murine organoids and donor-matched livers was, therefore, performed to assess both their similarity to liver tissue, and the expression of drug-metabolizing enzymes and transporters. This analysis quantified 4405 proteins across all sample types. Data are available via ProteomeXchange (PXD017986). Differentiation of organoids significantly increased the expression of multiple cytochrome P450, phase II enzymes, liver biomarkers and hepatic transporters. While the final phenotype of differentiated organoids is distinct from liver tissue, the organoids contain multiple drug metabolizing and transporter proteins necessary for liver function and drug metabolism, such as cytochrome P450 3A, glutathione-S-transferase alpha and multidrug resistance protein 1A. Indeed, the differentiated organoids were shown to exhibit increased sensitivity to midazolam (10–1000 µM) and irinotecan (1–100 µM), when compared to the undifferentiated organoids. The predicted reduced activity of HNF4A and a resulting dysregulation of RNA polymerase II may explain the partial differentiation of the organoids. Although further experimentation, optimization and characterization is needed relative to pre-existing models to fully contextualize their use as an in vitro model of drug-induced liver injury, hepatic organoids represent an attractive novel model of the response of the liver to xenobiotics. The current study also highlights the utility of global proteomic analyses for rapid and accurate evaluation of organoid-based test systems.
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Unlike most prior studies, which typically analyze snapshots of organoid development at single timepoints, this study employs a longitudinal approach to track dynamic transitions of iHLO populations.
“Unlike most prior studies, which typically analyze snapshots of organoid development at single timepoints14,15, this study employs a longitudinal approach to track the dynamic transitions of iHLO populations.”
From Temporal proteomic profiling of iPSC-derived human liver organoids reveals optimal maturation for drug metabolism and toxicology (2026) · cites this paper as [14]
The citation is attached to the characterization of prior studies as single-timepoint snapshots. In Results (‘Validation of mass spectrometry data by immunoblotting’; page unavailable), this paper explicitly includes samples from days four and eight to examine protein induction over time, so it is not an example of a single-timepoint study. The citing authors’ own longitudinal approach is not attributed to this source. (LLM, conf=0.85)
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Experimental — accuracy not yet measuredHowell et al. quantified 4,405 proteins in murine hepatic organoids and observed differentiation-dependent upregulation of CYP450 enzymes, hepatic transporters, and other metabolic proteins.
“For instance, Howell et al. quantified 4,405 proteins in murine hepatic organoids and observed differentiation-dependent upregulation of CYP450 enzymes, hepatic transporters, and other metabolic proteins, which parallels our observations in human iHLOs14.”
From Temporal proteomic profiling of iPSC-derived human liver organoids reveals optimal maturation for drug metabolism and toxicology (2026) · cites this paper as [14]
The Results sections on global protein expression and key hepatic proteins report 4,405 proteins identified across all samples and increased expression of multiple CYP450 enzymes, phase II enzymes, and transporters after organoid differentiation. The 4,405 count includes donor-matched liver samples, so the paper does not establish that all 4,405 were quantified in the organoids alone. Page numbers are unavailable in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredProteomics can offer a temporal roadmap of cellular differentiation and functional development in organoids.
“By profiling protein expression dynamics, proteomics can offer a temporal roadmap of cellular differentiation and functional development in organoids14–17.”
From Temporal proteomic profiling of iPSC-derived human liver organoids reveals optimal maturation for drug metabolism and toxicology (2026) · cites this paper as [14]
Liver organoids express key enzymes including members of the cytochrome P450 family and hepatic transporters, often at lower levels compared to native liver tissue.
“Studies have confirmed that liver organoids express key enzymes, including members of the cytochrome P450 (CYP450) family and hepatic transporters, though often at lower levels compared to native liver tissue14,15.”
From Temporal proteomic profiling of iPSC-derived human liver organoids reveals optimal maturation for drug metabolism and toxicology (2026) · cites this paper as [14]
The findings align with previous proteomic studies of liver organoids demonstrating their capacity to recapitulate liver-specific phenotypes.
“The findings from current study align with previous proteomic studies of liver organoids, which have demonstrated their capacity to recapitulate liver-specific phenotypes.”
From Temporal proteomic profiling of iPSC-derived human liver organoids reveals optimal maturation for drug metabolism and toxicology (2026) · cites this paper as [14]
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Sorted by citations
Liver organoids: established tools for disease modeling and drug development
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“By profiling protein expression dynamics, proteomics can offer a temporal roadmap of cellular differentiation and functional development in organoids 14–17 .”
- Authors
- Howell, L., Jenkins, R. E., Lynch, S., Duckworth, C., Kevin Park, B., & Goldring, C.
- Affiliations
- University of Liverpool (GB)
- Corresponding author
- Goldring, Christopher
- ORCID
- Venue
- Archives of Toxicology
- Published
- 2021-05-29
- Volume
- 95
- Issue
- 7
- Pages
- 2413-2430
- ISSN
- 0340-5761 (ISSN-L)
- 1432-0738
- PMC
- PMC8241807
- OpenAlex
- W3164452301
- Cited by
- 7
- References
- 6
- Citations by year
- 2026: 3 · 2024: 2 · 2023: 1 · 2022: 1
- FWCI
- 0.91
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Archives of Toxicology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Medical Research Council (grant number G0700654)
- Topics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Pharmacology › Drug-Induced Hepatotoxicity and Protection
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Pharmacology › Pharmacogenetics and Drug Metabolism
- Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
- Keywords
- hepatic organoids, drug metabolism, drug detoxification, drug-induced liver injury, cytochrome P450, drug-metabolizing enzymes, hepatic transporters, glutathione S-transferase, HNF4α, RNA polymerase II, midazolam, irinotecan, organoid differentiation, in vitro liver models, proteomic profiling
- MeSH terms
- Animals, Cell Differentiation, Cytochrome P-450 Enzyme System, Liver, Organoids, Proteomics, Mice
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