Translational resistance to amino acid starvation in breast cancer cells revealed by ribosome profiling.

Translation elongation is highly sensitive to amino acid availability, with deprivation causing ribosome pausing at cognate codons, suppression of the mammalian target of rapamycin (mTORC1) signaling pathway, and GCN2-mediated phosphorylation of eIF2α. However, cell-type heterogeneity in these responses remains unclear. Integrating ribosome profiling datasets across over ten human cell lines and multiple starvation conditions, we uncover translational resistance in breast cancer cells specifically under leucine and glutamine deprivation. Unlike non-breast cancer cells, breast cancer cells maintain ribosome occupancy on mRNAs with a 5' terminal oligopyrimidine tract (5'TOP mRNAs), indicating sustained mTORC1 activity, and exhibit attenuated codon-specific pausing. GCN2-eIF2α pathway activation varies among breast cancer lines. Downregulation of the cystine/glutamate transporter SLC7A11 correlates with this resistance, and its overexpression restores sensitivity by reducing S6K phosphorylation while enhancing eIF2α phosphorylation. Our findings reveal that breast cancer cells adaptively reshape translation regulation to withstand amino acid starvation, highlighting a potential metabolic vulnerability.