Induced Pluripotent Stem Cells in chemical safety testing- data management and bioinformatics workflows

Singh, Pranika. Induced Pluripotent Stem Cells in chemical safety testing- data management and bioinformatics workflows. 2022, Doctoral Thesis, University of Basel, Faculty of Science.


Official URL: https://edoc.unibas.ch/89643/

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In recent years, there has been a push toward the adoption of alternatives to animal-based approaches for chemical safety assessment. This has led to the development of better human in vitro models. Within the in3 project, human-induced pluripotent stem cells (iPSCs) were used in combination with in silico tools for application in mechanistic toxicity testing. Project-wide data managementand bioinformatics workflows were applied for the analysis of the transcriptomics data to uncover tissue-specific markers of toxicity and stress response pathways activated in iPSCs models against chemical exposure. In this thesis, first, the utility of iPSC-derived renal proximal tubule-like (PTL) cells in chemical testing was investigated. The cells were exposed to cadmium, arsenic, rotenone, tunicamycin, doxorubicin, amiodarone, and GW788388, and samples were collected at multiple time points. The time points were used to look at the temporal profile of the differentially expressed genes related to four important stress responses namely oxidative stress, metal response, p53 signaling pathway, and unfolded protein response. The results showed that iPSCs could unravel the activation of these stress responses. Oxidative stress response and metal response-related genes were found to be activated very early (around 1h-2h after exposure) in response to arsenic and cadmium but in later hours (around 12h-16h after exposure) in other compounds. Tunicamycin exposure led to the strongest expression levels of genes associated with unfolded protein response, which were activated very early (around 2h). Doxorubicin exposure led to the strongest expression levels of genes associated with the p53 signaling pathway showing activation from around 4h after exposure. Second, different iPSC models for the brain, blood-brain barrier, kidney, and liver were used to see their responses to paraquat (PQ) exposure. The pathways like oxidative stress and unfolded protein response known to be induced in response to PQ were found to be activated. Genes associated with these pathways showed a concentration-dependent increase for all the cell models. The brain model was found to be the most sensitive toward PQ based on the cytotoxicity curves. To investigate the reason for this, the expression level of transporters of PQ was checked as they are used by PQ to enter the cell. The amino acid transporters SLC3A2 and SLC7A11 showed high expression levels in the brain models leading to the high uptake of PQ in cells. In conclusion, these studies showed the potential of human- iPSCs in future studies for animal-free chemical safety assessment, determining the sensitivity of multiple models towards a chemical and signifying the applicability of temporal data in unraveling the evolution of mechanisms.
Advisors:Exner, Thomas and Wilks, Martin F. and Odermatt, Alex and Caiment, Florian
Faculties and Departments:05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Pharmazie > Molecular and Systems Toxicology (Odermatt)
05 Faculty of Science > Departement Pharmazeutische Wissenschaften > Pharmazie > Regulatory Toxicology (Wilks)
UniBasel Contributors:Wilks, Martin F. and Odermatt, Alex
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:14789
Thesis status:Complete
Number of Pages:141
Identification Number:
  • urn: urn:nbn:ch:bel-bau-diss147894
edoc DOI:
Last Modified:31 Oct 2023 02:30
Deposited On:02 Sep 2022 08:22

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