Abstract 2226: Prioritizing tumor types for clinical study of novel Sec61 inhibitors by searching for expression profiles of sensitive cell lines in tumor sample databases
Authors: Eric Lowe, R. Andrea Fan, Henry W.B. Johnson, Christopher J. Kirk, Dustin McMinn, Yu Qian, Brian Tuch
Journal: Cancer Research (2021)

Abstract Blockade of secreted and transmembrane protein translocation into the endoplasmic reticulum represents a potentially multifactorial approach to inhibiting tumor growth. We have shown that small molecule inhibitors of the Sec61 translocon can inhibit expression of autocrine growth factors, receptor oncogenes, and immune checkpoints. We nominated KZR-261 for clinical development and describe here bioinformatic analysis of in vitro cancer cell line screens and primary tumor samples that prioritizes potentially sensitive tumor types for clinical evaluation. Anti-tumor activity of KZR-834, a structurally related analog of KZR-261, was assessed in two cell line cytotoxicity screens totaling over 400 cell lines. Broad anti-cancer activity across tumor types was observed in both screens, with median IC50 of 0.39 µM and 0.15 µM. We next demonstrated that KZR-261 has equivalent activity to KZR-834 by testing it on a subset of 48 cell lines (R2=0.91). For cell lines with RNA-Seq gene expression profiles available in CCLE (N=232), we correlated sensitivity to KZR-834 with each gene's expression. This analysis revealed a modest correlation between expression and cell line sensitivity for many genes. However, even the gene with the strongest correlation between expression and sensitivity provided only a partial explanation for KZR-834 sensitivity (CCND2, Spearman ρ = 0.31, P-val = 10−4). Levels of Sec61 were not associated with cell line sensitivity (SEC61A1, ρ = -0.05, P-val = 0.57). We therefore surveyed the gene-level results for enrichment of over 7,000 modules by performing fGSEA analysis. Enriched modules were hierarchically clustered revealing 6 primary clusters associated with sensitivity. The 6 clusters highlighted processes such as transcription, translation, metabolism, golgi vesicle transport, as well as genes encoding proteins that are secreted or plasma membrane localized. While fGSEA did not identify basal levels of ER stress as a process correlated with sensitivity, cell lines treated with KZR-834 have consistently shown activation of ER stress pathways at the mRNA and protein level, which led to its inclusion in subsequent analyses. Modules representing these 7 processes were then utilized to search tumor and normal tissue gene expression data from TCGA, TARGET and GTEx. Tumor types such as ALL, DLBCL, uveal and cutaneous melanoma, and mesothelioma were more enriched for expression of these modules than other tumor types and the vast majority of normal tissues. Our novel small molecule inhibitors of Sec61 dependent protein translocation exhibit broad anti-tumor activity in vitro. Large cell line screens and bioinformatic analyses identifying tumor intrinsic sensitivities led to a prioritized list of potentially sensitive tumor types that has guided tumor type selection for our initial Phase 1 clinical trial of KZR-261 in solid tumors. Citation Format: Eric Lowe, R. Andrea Fan, Henry W.B. Johnson, Christopher J. Kirk, Dustin McMinn, Yu Qian, Brian Tuch. Prioritizing tumor types for clinical study of novel Sec61 inhibitors by searching for expression profiles of sensitive cell lines in tumor sample databases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2226.