Nicotinamide N-methyltransferase promotes drug resistance in lung cancer, as revealed by nascent proteomic profiling

Kinase inhibitors have achieved great success in targeted Cancer therapy, yet the evident limitations in their effectiveness persist due to therapeutic resistance. To gain insight into the molecular mechanisms and thwart resistance, we profiled the time-resolved nascent protein perturbations in response to drug therapy using metabolic labeling and facilitated the identification of 2238 proteins via liquid chromatography tandem mass spectrometry (LC-MS/MS). Among these, 51 proteins exhibited upregulation, whereas 105 proteins showed downregulation following a 24-h drug treatment. Clustering analysis revealed that the differential proteins were mainly enriched in metabolic-related pathways. Combined with changes in whole-protein levels, we noticed significant fluctuations in the metabolism-related protein nicotinamide N-methyltransferase (NNMT). Additionally, NNMT overexpression diminished drug effectiveness, whereas its inhibition enhanced therapeutic efficacy. An increase in NNMT was also found in drug-resistant cells, and the NNMT Inhibitor JBSNF-000088 inhibited the proliferation of resistant cells. Subsequent phosphoproteomic analysis indicated that the effects of NNMT overexpression on transcription factors, proteins involved in the Rho GTPases cycle, and cell-cycle-related proteins may be related to tumor resistance. In summary, our study provides unique insights into nascent protein perturbations during the initial stages of drug therapy and identified NNMT as a promising target for delaying and overcoming therapeutic resistance.

EGFR inhibitor; NNMT; cancer drug resistance; nascent proteome; phosphorylation.