Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in NSCLC

Targeted therapy is effective in many tumor types including lung cancer, the leading cause of cancer mortality. Paradigm defining examples are targeted therapies directed against non-small cell lung cancer (NSCLC) subtypes with oncogenic alterations in EGFR, ALK and KRAS. The success of targeted therapy is limited by drug-tolerant persister cells (DTPs) which withstand and adapt to treatment and comprise the residual disease state that is typical during treatment with clinical targeted therapies. Here, we integrate studies in patient-derived and immunocompetent lung cancer models and clinical specimens obtained from patients on targeted therapy to uncover a focal adhesion kinase (FAK)-YAP signaling axis that promotes residual disease during oncogenic EGFR-, ALK-, and KRAS-targeted therapies. FAK-YAP signaling inhibition combined with the primary targeted therapy suppressed residual drug-tolerant cells and enhanced tumor responses. This study unveils a FAK-YAP signaling module that promotes residual disease in lung cancer and mechanism-based therapeutic strategies to improve tumor response. RNA sequencing in (1) EGFR-mutant PC9 cells, ALK fusion-positive H3122 cells, and KRAS-mutant H358 cells upon drug treatment. The following conditions are available per each cell line: treatment with 0.1 % DMSO for 48 hours in parental cells, treatment with targeted inhibitor for 48 hours in parental cells, treatment with targeted inhibitor for ≥ 9 days in persister cells, treatment with targeted inhibitor in acquired resistant cells. Relates to Fig. 2o, Supplemental Fig. 2d. (2) Isogenic EGFR-mutant PC9-C2 and H1975-B10 prior to treatment (t0) and in osimertinib persisters (d9). (3) EGFR-mutant PC9 cells comparing empty vector control cells (EV), YAP-WT overexpressing cells, hyperactive YAP-5SA overexpressing cells, and inactive YAP-S94A cells. (4) EGFR-mutant PC9 osimertinib persister cells and ALK fusion-positive H3122 alectinib persister cells upon combinatorial treatment with TEAD inhibitor VT104. Relates to Suppl. Figure 4: Gene set enrichment analysis (GSEA) was performed using the YAP-5SA_UP gene set (Supplementary Table 3) on RNAseq expression data from PC9 osimertinib DTPs and H3122 alectinib DTPs, both treated with 10 µM VT104 for 24 h. (5) EGFR-mutant organoid models TH107 and TH330 comparing cells treated with 0.1% DMSO for 3 days and with 1 µM osimertinib for 11 days; relates to Suppl. Figure 7e: RNAseq expression data of the EGFR-mutant TH107 PDO model, comparing untreated DMSO control (DMSO) versus osimertinib persisters (D9). (6) EGFR-mutant PDX TH021 and ALK fusion-positive LG0812 comparing vehicle and TKI treated tumors at treatment endpoint; relates to Supplemental Fig. 8(d&e): Gene set enrichment analysis for the YAP-5SA_UP gene set (Supplementary Table 3) using RNAseq expression data of the EGFR-mutant TH021 PDX model (d) and ALK fusion-positive LG0812 PDX model (e), comparing vehicle control (VEH) versus treatment group (TKI).