Screening for variable drug responses using human iPSC cohorts
Melpomeni Platani, Hao Jiang, Lindsay Davidson, Santosh Hariharan, Regis Doyonnas, Angus I. Lamond, Jason R. Swedlow
Abstract
We have developed a laboratory-based drug screening platform that uses a cohort of human induced pluripotent stem cell (hiPSC) lines, derived from different donors, to predict variable drug responses of potential clinical relevance. This builds on recent findings that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins, whose expression levels reflect the genetic identity of the donor.
Introduction
Most current drug development pipelines involve an initial laboratory-based research phase, in which disease-relevant molecular targets are identified (usually proteins) and then either small molecules, or biological effectors (e.g., antibodies), are characterised that specifically bind to, or otherwise modulate, the targets. Promising drug candidates are then progressed from animal models to human clinical trials, where they must be evaluated for efficacy and possible toxicity in human patients before they can be certified for use by regulatory authorities [1–3].
Materials and method
Cell culture
Human iPSC lines used in this study were from the HipSci cohort (4). Feeder-free human iPSC lines were cultured in Essential 8 (E8) medium (E8 complete medium supplemented with (50x) E8 supplement ThermoFisher-A1517001) on tissue-culture dishes coated with 10 µg/cm2 of reduced Growth Factor Basement Membrane matrix (Geltrex, ThermoFisher A1413202 resuspended in basal medium DMEM/F12 Thermo Fisher 21331020). Medium was changed daily.
Results
Establishing Pluripotency in hiPSC Cohorts in High-Throughput Format
To test whether we could detect and characterize variable drug responses across a cohort of hiPSC lines from different donors, the high throughput Cell Painting assay [16] was first adapted for use with hiPSC lines grown in the pluripotent state. We reasoned that an image-based Cell Painting assay could be used to detect variable responses and stratify cell lines accordingly, followed by using quantitative MS-based proteomics to identify potential mechanisms causing the variable responses (see Fig 1A).
Discussion
We have established, to our knowledge, the first laboratory pipelines for the systematic analysis of population-level variable drug responses, using a cohort of hiPSC lines, derived from multiple, healthy donors. Previous work has described culturing hiPSCs from a single patient in 384-well plate for drug screening, In this study, we have used a cohort of hiPSC lines from many different donors and Cell Painting to garner significantly more information from the screens [12,49]. This pipeline provides a ‘genetically-informed’, high-throughput assay for identifying and characterising variable drug responses in human cells, using Cell Painting and quantitative proteomics. This analysis provides an initial quantitative measure of variable response across a cohort of hiPSC lines [50].
Acknowledgments
We thank members of the National Phenotypic Screening Centre and Human Pluripotent Stem Cell Facility at the University of Dundee for invaluable help and advice. We thank University of Dundee’s School of Life Sciences for their support of this project.
Citation: Platani M, Jiang H, Davidson L, Hariharan S, Doyonnas R, Lamond AI, et al. (2025) Screening for variable drug responses using human iPSC cohorts. PLoS One 20(5): e0323953. https://doi.org/10.1371/journal.pone.0323953
Editor: Nanako Kawaguchi, Tokyo Women's Medical University, JAPAN
Received: January 10, 2025; Accepted: April 17, 2025; Published: May 30, 2025
Copyright: © 2025 Platani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: Image data was deposited to the Image Data Resource (https://idr.openmicroscopy.org) under accession number idr0169. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium, via the PRIDE partner repository with the dataset identifier PXD050194.
Funding: This work was supported by the Biotechnology and Biological Sciences Research Council [grant numbers BB/V010948/1, APP3732 to AIL]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: The authors Melpomeni Platani, Angus I. Lamond and Jason R. Swedlow would like to declare a conflict of interest through their affiliation with Tartan Cell Technologies, Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
