Memory effects of prior subculture may impact the quality of multiomic perturbation profiles
- Author(s)
- Patricia Janker-Bortel, Gerhard Hagn, Lukas Skos, Andrea Bileck, Verena Paulitschke, Philipp Paulitschke, Lion Gleiter, Thomas Mohr, Christopher Gerner, Samuel M. Meier-Menches
- Abstract
Mass spectrometry-based omics technologies are increasingly used in perturbation studies to map drug effects to biological pathways by identifying significant molecular events. Significance is influenced by fold change and variation of each molecular parameter, but also by multiple testing corrections. While the fold change is largely determined by the biological system, the variation is determined by experimental workflows. Here, it is shown that memory effects of prior subculture can influence the variation of perturbation profiles using the two colon carcinoma cell lines SW480 and HCT116. These memory effects are largely driven by differences in growth states that persist into the perturbation experiment. In SW480 cells, memory effects combined with moderate treatment effects amplify the variation in multiple omics levels, including eicosadomics, proteomics, and phosphoproteomics. With stronger treatment effects, the memory effect was less pronounced, as demonstrated in HCT116 cells. Subculture homogeneity was controlled by real-time monitoring of cell growth. Controlled homogeneous subculture resulted in a perturbation network of 321 causal conjectures based on combined proteomic and phosphoproteomic data, compared to only 58 causal conjectures without controlling subculture homogeneity in SW480 cells. Some cellular responses and regulatory events were identified that extend the mode of action of arsenic trioxide (ATO) only when accounting for these memory effects. Controlled prior subculture led to the finding of a synergistic combination treatment of ATO with the thioredoxin reductase 1 inhibitor auranofin, which may prove useful in the management of NRF2-mediated resistance mechanisms.
- Organisation(s)
- Department of Analytical Chemistry, Joint Metabolome Facility, Department of Inorganic Chemistry
- External organisation(s)
- Medizinische Universität Wien, PHIO scientific GmbH, Ludwig-Maximilians-Universität München, Vienna Doctoral School in Chemistry (DoSChem)
- Journal
- Proceedings of the National Academy of Sciences of the United States of America
- Volume
- 121
- ISSN
- 0027-8424
- DOI
- https://doi.org/10.1073/pnas.2313851121
- Publication date
- 07-2024
- Peer reviewed
- Yes
- Austrian Fields of Science 2012
- 104002 Analytical chemistry, 106037 Proteomics
- Keywords
- ASJC Scopus subject areas
- General
- Portal url
- https://ucrisportal.univie.ac.at/en/publications/c4cef9a5-9ba6-4c38-9af5-649d927ee9cf