A four-gene signature identifies TKI-induced persister cells and uncovers a ZLN005-induced pyroptotic vulnerability via the GSDME pathway in EGFR-mutant lung cancer
TL;DR
Public transcriptomic datasets from tumour cell-based models treated with EGFR inhibitors or other targeted agents within the receptor tyrosine kinase (RTK)/RAS/MAPK pathway were integrated with machine-learning-based feature selection, survival analysis and Cancer Dependency Map-based pharmacogenomic screening to define the transcriptional and metabolic features of targeted therapy-induced persister cells.
Abstract
Drug-tolerant persister cells represent a major barrier to durable responses in cases of epidermal growth factor receptor (EGFR)-mutant lung adenocarcinoma treated with tyrosine kinase inhibitors. To define the molecular features and actionable vulnerabilities of this cell state, public transcriptomic datasets from tumour cell-based models treated with EGFR inhibitors or other targeted agents within the receptor tyrosine kinase (RTK)/RAS/MAPK pathway were integrated with machine-learning-based feature selection, survival analysis and Cancer Dependency Map-based pharmacogenomic screening. The present study also performed experimental validation of identified genes and drugs in PC-9 and HCC827 cell models. A four-gene persister-associated gene signature comprising B-cell translocation gene 1 protein, inhibitor of growth protein 4, proline-rich nuclear receptor coactivator 1 and calcium-binding and coiled-coil domain-containing protein 1 was identified, which defined a targeted therapy-induced persister state and associated with poor patient survival. Functional validation using reverse transcription-quantitative PCR, doxycycline-inducible short hairpin RNA knockdown and β-galactosidase staining assays demonstrated rapid induction of these genes during osimertinib treatment and showed that depletion of each gene markedly impaired drug-tolerant persister cell formation. Pharmacogenomic analysis identified ZLN005, a peroxisome proliferator-activated receptor γ coactivator-1α agonist, as a candidate metabolic modulator that synergized with osimertinib to reduce persister cell viability. Mechanistically, ZLN005 enhanced mitochondrial oxidative metabolism and reactive oxygen species accumulation, leading to caspase-3 activation and gasdermin E-associated pyroptotic cell death. Collectively, these findings defined the transcriptional and metabolic features of targeted therapy-induced persister cells and revealed a metabolic vulnerability to ZLN005 in EGFR-mutant lung adenocarcinoma.