Abstract
We have previously identified selective upregulation of the mevalonate pathway genes upon inhibition of oxidative phosphorylation (OXPHOS) in quiescent cancer cells. Using mass spectrometry-based proteomics, we here investigated whether these responses are corroborated on the protein level and whether proteomics could yield unique insights into context-dependent biology. HCT116 colon carcinoma cells were cultured as monolayer cultures, proliferative multicellular tumor spheroids (P-MCTS), or quiescent (Q-MCTS) multicellular tumor spheroids and exposed to OXPHOS inhibitors: nitazoxanide, FCCP, oligomycin, and salinomycin or the HMG-CoA-reductase inhibitor simvastatin at two different doses for 6 and 24 h. Samples were processed using an in-depth bottom-up proteomics workflow resulting in a total of 9286 identified protein groups. Gene set enrichment analysis showed profound differences between the three cell systems and confirmed differential enrichment of hypoxia, OXPHOS, and cell cycle progression-related protein responses in P-MCTS and Q-MCTS. Treatment experiments showed that the observed drug-induced alterations in gene expression of metabolically challenged cells are not translated directly to the protein level, but the results reaffirmed OXPHOS as a selective vulnerability of quiescent cancer cells. This work provides rationale for the use of deep proteome profiling to identify context-dependent treatment responses and encourages further studies investigating metabolic processes that could be co-targeted together with OXPHOS to eradicate quiescent cancer cells.
Highlights
Cancer cells are usually characterized by their increased proliferation, resistance to apoptosis, invasiveness, and poor differentiation
We demonstrate the influence of different culture conditions by profiling the colon cancer cell line HCT116 grown as Q-multicellular tumor spheroids (MCTS), proliferative multicellular tumor spheroids (P-MCTS), and monolayer cells
The obtained list of identified proteins was further reduced to proteins with a high-protein false discovery rate (FDR) confidence and at least two unique peptides (Figure 7D)
Summary
Cancer cells are usually characterized by their increased proliferation, resistance to apoptosis, invasiveness, and poor differentiation. MCTS are usually generated from cell lines while tumor organoids are formed from primary cancer cells. Because of the cost of organoid development and expansion and limited cellular material availability, MCTS can more and reproducibly be used in the large experimental setup, for example, high-throughput drug screening,[4−6] and have been a valuable model for the studies of clinically relevant aspects of cancer biology, as they resemble morphological, functional, and microenvironmental features of in vivo tumor tissues.[7] most commonly used spheroid models are highly proliferative MCTS (PMCTS), as they are usually maintained in standard nutrientrich culture media.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
