Abstract 3538: Endogenous HiBiT-tagging of PAX3-FOXO1 identifies potent suppressors of PAX3-FOXO1 protein levels by high-throughput screening
Authors: Kim Yong Yean , Hawley Robert G. , Churiwal Mehal , Hawley Teresa S. , Evans Christine N. , Chari Raj , Milewski David , Sinniah Ranuka , Song Young K. , Chou Hsien-Chao , Wen Xinyu , Pang Ying , Wu Jing , Thomas Craig J. , Wei Jun S. , Ceribelli Michele , Khan Javed 
Published: April 2023

Abstract
Background: Oncogenic fusion genes are attractive therapeutic targets due to their tumor-specific expression and driver roles in cancers. PAX3-FOXO1 (P3F) is the dominant oncogenic driver of fusion-positive rhabdomyosarcoma (FP-RMS) with no targeted therapy. We developed methods to directly measure endogenous P3F protein levels amenable to high-throughput drug screens to identify suppressors of P3F.
Methods: HiBiT tag, an 11 amino acid peptide of the small fragment of NanoLuc luciferase, was inserted into the endogenous P3F using CRISPR-Cas9 in FP-RMS cell lines RH4 and SCMC. Western analysis was used for HiBiT tag validation and confirmation of P3F suppression. RNA-seq and ChIP-seq were used to assess transcriptomics and DNA binding of HiBiT-tagged P3F (P3F-HiBiT) respectively. High-throughput drug screen using Nano-Glo luciferase assay was performed using the Mechanism Interrogation PlatE (MIPE 5.0) drug library, which included 2,480 drugs with known mechanisms of action. CellTiter-Glo was used to monitor cell viability. We identified drugs that suppressed P3F by Nano-Glo without acute cytotoxicity by CellTiter-Glo at an early 24-hour timepoint. Mouse xenograft model of FP-RMS was used to investigate in vivo efficacy of top hits.
Results: We validated HiBiT tagging of P3F and not the wild-type FOXO1 by Western analysis. We showed that the HiBiT tag did not change the function of P3F by transducing human fibroblasts with P3F-HiBiT versus unmodified P3F. Gene Set Enrichment Analysis (GSEA) of RNA-seq showed that P3F-HiBiT activated the same downstream target genes as unmodified P3F. ChIP-seq using HiBiT antibody in HiBiT-tagged FP-RMS cell lines RH4 and SCMC matched the genomic locations from ChIP-seq with P3F antibody in parental RH4 and SCMC. Using a cutoff of Area Under the Curve (AUC) of CellTiter-Glo - AUC of Nano-Glo &gt; 90, in both RH4 and SCMC, identified 182 compounds. Filtering for drugs with ≥ 3 hits for the same target identified 14 drug classes that suppressed P3F protein level including HDAC inhibitors (3), mTOR inhibitors (4), CDK inhibitors (8), and BRD4 inhibitors (3). One top hit was the CDK inhibitor TG02 (Zotiraciclib), currently in human trials. TG02 suppressed P3F protein levels by Nano-Glo and Western analysis. We confirmed induction of apoptosis by PARP cleavage in a panel of FP-RMS cell lines. GSEA analysis of RNA-seq after treatment with TG02 showed marked suppression of P3F target gene sets. TG02 also significantly delayed tumor progression of established tumors in a mouse xenograft model of FP-RMS without weight loss.
Conclusion and Future Directions:By HiBiT tagging the fusion oncogene P3F, we identified 182 compounds that suppress P3F levels of which TG02 was a top hit that also showed in vivo efficacy. Drug combination studies are currently underway to identify synergistic suppressors of P3F protein levels that can be translated into clinical trials.
Citation Format: Yong Yean Kim, Robert G. Hawley, Mehal Churiwal, Teresa S. Hawley, Christine N. Evans, Raj Chari, David Milewski, Ranuka Sinniah, Young K. Song, Hsien-Chao Chou, Xinyu Wen, Ying Pang, Jing Wu, Craig J. Thomas, Jun S. Wei, Michele Ceribelli, Javed Khan. Endogenous HiBiT-tagging of PAX3-FOXO1 identifies potent suppressors of PAX3-FOXO1 protein levels by high-throughput screening. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3538.