Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids

Abstract

Cancer cell lines grown as two-dimensional (2D) cultures have been an essential model for studying cancer biology and anticancer drug discovery. However, 2D cancer cell cultures have major limitations, as they do not closely mimic the heterogeneity and tissue context of in vivo tumors. Developing three-dimensional (3D) cell cultures, such as multicellular tumor spheroids, has the potential to address some of these limitations. Here, we combined a high-throughput gene expression profiling method with a tumor spheroid-based drug-screening assay to identify context-dependent treatment responses. As a proof of concept, we examined drug responses of quiescent cancer cells to oxidative phosphorylation (OXPHOS) inhibitors. Use of multicellular tumor spheroids led to discovery that the mevalonate pathway is upregulated in quiescent cells during OXPHOS inhibition, and that OXPHOS inhibitors and mevalonate pathway inhibitors were synergistically toxic to quiescent spheroids. This work illustrates how 3D cellular models yield functional and mechanistic insights not accessible via 2D cultures.

A novel inhibitor of tumorspheres reveals the activation of the serine biosynthetic pathway upon mitochondrial inhibition

“…Although this is a small increment, it actually represents a potentially greater impact, since restricting proliferation by mitochondrial inhibitors is not apparent, or at least very modest in nutrient-rich cell culture conditions [31,32]. A recent study in HCT116 tumourspheres found that limiting activation of the mevalonate pathway enhanced the efficacy of mitochondrial inhibitors [39]. These findings, along with ours, indicate that limiting or targeting activated compensatory pathways could be a strategy to enhance the efficacy of mitochondrial inhibitors.…”

Nitazoxanide inhibits paramyxovirus replication by targeting the Fusion protein folding: role of glycoprotein-specific thiol oxidoreductase ERp57

“…The possibility that defects in HN-protein maturation may also participate in thiazolide antiviral activity in SeV-infected cells is currently under investigation. In addition, it should be noted that nitazoxanide was found to inhibit oxidative phosphorylation leading to decreased ATP levels in cancer cells 28 , 29 . Since metabolic energy is known to be required for correct disulfide bond formation and folding of several proteins in the ER 30 – 32 , it is possible that lower ATP levels in NTZ-treated cells may contribute to F-protein misfolding in our model.…”

Transcriptomic Profiling of 3D Glioblastoma Tumoroids for the Identification of Mechanisms Involved in Anticancer Drug Resistance

“…Several RNA-sequencing studies demonstrated significant, tumor-relevant molecular changes induced by 3D cell culture (12,22,23). Glioblastoma spheroids in 3D culture mimicked in vivo tissues, organs and even patient tumors, providing in vivo 34: 199-211 (2020) 204 similar cellular properties including hypoxic gradients, cellular heterogeneity with both slow-dividing cells and proliferative tumor bulk (24,25) and higher drug resistance (10).…”