A multiplex single-cell RNA-seq pharmacotranscriptomics pipeline for drug discovery

We report a pipeline for high-throughput pharmacotranscriptomic profiling via 96-plexed single-cell RNA-sequencing (scRNA-Seq) using Cell Hashing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of PI3K/AKT/mTOR inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this is mediated by the upregulation of caveolin-1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of PI3K/AKT/mTOR- and EGFR-targeting agents for HGSOC with CAV1/EGFR expression. JHOS2, PDC2, and PDC3 cells were treated for 24 hours with 45 drugs (and DMSO as control) in duplicates using a drug concentration above EC50 based on DSRT screens, which was likely able to elicit a transcriptional response across all drugs. Following drug treatments, cells in each well were labeled with a unique pair of β2microglobulin (B2M) and CD298 antibody-oligo conjugates from a set of 20 (12 for the columns and 8 for the rows of a 96-well plate) before samples pooling for multiplexed scRNA-Seq. Drug name (concentration in µM): AR-42 (10 µM); AT 101 (100 µM); AT9283 (1 µM); AZD-8055 (1 µM); AZD-8186 (1 µM); Belinostat (10 µM); BI 2536 (0.1 µM); Birabresib (10 µM); Birinapant (0.1 µM); BMS-754807 (10 µM); Buparlisib (10 µM); Cobimetinib (1 µM); Copanlisib (1 µM); Dactolisib (1 µM); Danusertib (10 µM); Dasatinib (1 µM); Dinaciclib (0.1 µM); ENMD-2076 (10 µM); Fedratinib (10 µM); Gedatolisib (0.1 µM); I-BET151 (10 µM); Ipatasertib (10 µM); JQ1 (10 µM); LY3009120 (2.5 µM); Milciclib (10 µM); Niraparib (10 µM); NVP-BGT226 (0.1 µM); NVP-LCL161 (2.5 µM); OTS167 (0.1 µM); Pacritinib (10 µM); PD0325901 (1 µM); PF-00477736 (10 µM); PF-03758309 (10 µM); Pictilisib (10 µM); Pracinostat (10 µM); Quisinostat (1 µM): Ralimetinib (10 µM); SCH772984 (10 µM); Selinexor (10 µM); SNS-032 (1 µM); Talazoparib (1 µM); TGX-221 (10 µM); UCN-01 (1 µM); Volasertib (1 µM); ZSTK474 (10 µM). JHOS2 raw sequencing data are provided with this record. For the patient-derived cells raw sequencing data, please contact the corresponding author.