Proteomic Profiling Reveals How Physiological Media Reshape Cancer Cell Proteomes and Signaling Networks.

Area of Science:

• Cancer Biology
• Proteomics
• Metabolomics

Background:

• Altered cellular metabolism is a key cancer characteristic, making metabolic enzymes therapeutic targets.
• Metabolic inhibitors show limited success due to discrepancies between standard cell culture media and physiological nutrient conditions.
• Human plasma-like medium (HPLM) mimics in vivo metabolite concentrations but its impact on cellular proteomes is not well understood.

Purpose of the Study:

• To investigate the effects of HPLM on cellular proteomes and signaling pathways in cancer cell lines.
• To compare proteomic and phosphoproteomic profiles of cancer cells cultured in DMEM versus HPLM.
• To identify cell-type-specific adaptations in metabolic networks and mitochondrial proteomes under physiological conditions.

Main Methods:

• Quantitative proteomics (TMTpro) and phosphoproteomics were performed on nine cancer cell lines.
• Cells were cultured in standard DMEM and human plasma-like medium (HPLM).
• Over 10,000 proteins and 24,000 phosphorylation sites were quantified with high reproducibility.

Main Results:

• HPLM induced significant, cell-type-specific remodeling of metabolic networks, mitochondrial proteomes, and signaling pathways.
• Universal responses included decreased mTORC1 and CDK activity, but metabolic enzyme expression varied significantly.
• Consistent reductions in folate metabolism and pyrimidine salvage enzymes were observed across cell types.
• Mitochondrial proteome composition and morphology showed cell-type-specific adaptations.
• Phosphoproteomic analysis identified kinase signaling networks linked to metabolic alterations.

Conclusions:

• Cellular proteomes and signaling pathways undergo profound, cell-type-specific remodeling when cultured in physiological media like HPLM.
• The choice of culture medium significantly impacts metabolic enzyme expression and cellular responses, potentially affecting drug efficacy.
• This study provides a valuable resource for cancer metabolic research using physiological media, emphasizing the importance of cell-specific variability.