Inhibition of Karyopherin β1-mediated nuclear import of lineage-defining TFs in small cell lung cancer

Extensive genomic studies support the classification of small cell lung cancer (SCLC) into subtypes based on expression of lineage-defining transcription factors including ASCL1 and NEUROD1, which together account for ~80% of this disease. ASCL1 and NEUROD1 activate SCLC oncogene expression and drive distinct transcriptional programs. ASCL1 is also required for tumorigenesis in SCLC mouse models, and both ASCL1 and NEUROD1 maintain the in vitro growth and oncogenic properties of ASCL1+ or NEUROD1+ SCLC cell lines. Strategies to inhibit ASCL1 and NEUROD1 may therefore represent an attractive, targeted SCLC therapy and provide a tool to investigate the underlying plasticity of the predominant SCLC subtypes. However, ASCL1 and NEUROD1 have long been considered “undruggable” vulnerabilities. Here, we use a proteomic approach to identify Karyopherin β1 (KPNB1) as a nuclear import receptor for ASCL1 and NEUROD1 in SCLC, and demonstrate that the inhibition of KPNB1 using a variety of genetic or pharmacological approaches leads to impaired ASCL1 and NEUROD1 nuclear accumulation and transcriptional activity. Pharmacological targeting of KPNB1 preferentially disrupts ASCL1/NEUROD1+ SCLC cell line growth in vitro and ASCL1+ tumor growth in an in vivo patient derived xenograft (PDX) model of SCLC. Bulk mRNA profiles of SCLC-A subtype NCI-H2107 cell lines (Empty Vector n=2 for CRISPRi ASCL1 experiment and CRISPRi KPNB1 experiment, CRISPRi ASCL1 n=2, CRISPRi KPNB1 n=2), SCLC-A subtype JHU-LX44 PDX samples (Vehicle n=2, INI-43-treated n=3), SCLC-N subtype JHU-LX22 PDX samples (Vehicle n=3, INI-43-treated n=3), and RPM GEMM tumor samples (Control n=6, INI-43 treated n=7). "Control" = Vehicle treated or untreated.