Namhee Yu^1†, Mihwa Hwang^1†, Youngjoo Lee^1†, Bo Ram Song¹, Eun Hye Kang¹, Hanna Sim¹, Beung‑Chul Ahn¹, Kum Hui Hwang¹, Jihyun Kim², Sehwa Hong¹, Sunshin Kim^1*, Charny Park^1* and Ji‑Youn Han^1*

1Research Institute, National Cancer Center, Goyang‑si, Gyeonggi‑do 10408, Republic of Korea. 
2Department of Precision Medicine, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Republic of Korea. 

†Namhee Yu, Mihwa Hwang and Youngjoo Lee contributed equally to this work.
*Correspondence: Sunshin Kim, Charny Park, Ji‑Youn Han

Background: A pharmacogenomic platform using patient-derived cells (PDCs) was established to identify the underlying resistance mechanisms and tailored treatment for patients with advanced or refractory lung cancer.

Methods: Drug sensitivity screening and multi-omics datasets were acquired from lung cancer PDCs (n = 102). Integrative analysis was performed to explore drug candidates according to genetic variants, gene expression, and clinical profiles.

Results: PDCs had genomic characteristics resembled with those of solid lung cancer tissues. PDC molecular subtyping classified patients into four groups: (1) inflammatory, (2) epithelial-to-mesenchymal transition (EMT)-like, (3) stemness, and (4) epithelial growth factor receptor (EGFR)-dominant. EGFR mutations of the EMT-like subtype were associated with a reduced response to EGFR-tyrosine kinase inhibitor therapy. Moreover, although RB1/TP53 mutations were significantly enriched in small-cell lung cancer (SCLC) PDCs, they were also present in non-SCLC PDCs. In contrast to its effect in the cell lines, alpelisib (a PI3K-AKT inhibitor) significantly inhibited both RB1/TP53 expression and SCLC cell growth in our PDC model. Furthermore, cell cycle inhibitors could effectively target SCLC cells. Finally, the upregulation of transforming growth factor-β expression and the YAP/TAZ pathway was observed in osimertinib-resistant PDCs, predisposing them to the EMT-like subtype. Our platform selected XAV939 (a WNT-TNKS-β-catenin inhibitor) for the treatment of osimertinib-resistant PDCs. Using an in vitro model, we further demonstrated that acquisition of osimertinib resistance enhances invasive characteristics and EMT, upregulates the YAP/TAZ-AXL axis, and increases the sensitivity of cancer cells to XAV939.

Conclusions: Our PDC models recapitulated the molecular characteristics of lung cancer, and pharmacogenomics analysis provided plausible therapeutic candidates.