DeepBiome Therapeutics (United States)

Abstract Aberrant expression of the transcription factor MYC is found in most cancers including non-small cell lung cancer (NSCLC) and has critical roles in a wide range of oncogenic processes including immune evasion and EGFR inhibitor resistance. Despite MYC’s therapeutic attractiveness, potent inhibitors of MYC activity have been elusive, due to its intrinsically disordered protein structure and tightly autoregulated expression. We have developed NSCLC-specific programmable epigenomic mRNA therapy, termed a MYC Omega epigenomic controller (NSCLC MYC-OEC) that is designed to target the insulated genomic domain of MYC. We have previously shown that NSCLC MYC-OEC effectively downregulates MYC expression pre-transcriptionally and have demonstrated that NSCLC MYC-OEC inhibits NSCLC patient-derived organoid viability in vitro and abrogates xenograft tumor growth in vivo. To identify combination treatments with NSCLC MYC-OEC, we retrospectively evaluated baseline MYC expression and real-world progression-free survival (PFS) in a cohort of 283 NSCLC patients treated with pembrolizumab, an anti-PD1 monoclonal antibody. This analysis revealed that NSCLC patients with MYC-overexpressing tumors exhibited shorter PFS when treated with pembrolizumab. Moreover, analysis of PD1 or PD-L1 transcript levels in tumors from 13,230 lung adenocarcinoma patients revealed a significant positive correlation between PD1 or PD-L1 and MYC mRNA levels, consistent with a role for MYC in regulation of the immune response. In vivo evaluation of NSCLC MYC-OEC activity and immune checkpoint immunotherapy (ICI) treatment of preclinical Lewis lung carcinoma syngeneic tumor models demonstrated that the combination of NSCLC MYC-OEC with anti-PD-L1 antibody enhanced inhibition of tumor growth and prolonged survival over administration when compared to either NSCLC MYC-OEC or anti-PD-L1 antibody monotherapy. Retrospective analysis of a cohort of 301 NSCLC patients also showed that patients with MYC-overexpressing tumors exhibited significantly shorter PFS when treated with osimertinib, a third generation EGFR inhibitor. To further understand this, we investigated the effects of NSCLC MYC-OEC and osimertinib treatment alone or in combination in EGFR mutant cells, H1975 and PC9. While NSCLC MYC-OEC and osimertinib monotherapy treatments resulted in downregulation of MYC protein expression in both cell lines, combination treatment led to a significantly greater decrease in MYC expression. Furthermore, the combination synergistically reduced H1975 and PC9 cell viability in vitro and led to a significantly greater inhibition of H1975 xenograft growth relative to each single agent in vivo. Together, these data provide preclinical proof-of-concept in NSCLC for development of OEC-mediated pre-transcriptional epigenomic inhibition of MYC expression in combination with immune checkpoint and EGFR inhibitors. Furthermore, these findings suggest that NSCLC MYC-OEC combination with ICI or EGFR-targeted therapy may improve patient outcomes. Citation Format: Defne Yarar, Eugine Lee, Padraich Flahardy, Cameron Vergato, Graeme Hodgson, Thomas McCauley. Targeted epigenomic inhibition of MYC enhances responses to immune checkpoint and EGFR inhibitors in preclinical models of NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C104.

Abstract Hepatocellular carcinoma (HCC), the fourth leading cause of cancer deaths, represents an unmet medical need with few therapeutic options. Sorafenib has been used as a systemic therapy for HCC for >10 years but patients frequently develop resistance with oncogenic c-MYC (MYC) identified as a correlating prognostic factor. MYC over-expression is associated with aggressive disease in up to ~70% of HCC. While MYC represents an attractive therapeutic target, it has historically been considered undruggable, largely because it lacks a structured binding pocket and its expression is tightly autoregulated. The MYC gene and its regulatory elements are part of an insulated genomic domain (IGD), a chromatin looping region anchored by CTCF. Here we describe our approach to specifically modulate levels of MYC expression by utilizing targeted mRNA-encoded proteins, Omega Epigenomic Controllers (OECs), to mediate epigenetic regulation while potentially overcoming MYC autoregulation. For screening, putative OECs were directed to 2 loci on the MYC IGD. Identified target loci were used to design optimized OECs, including development candidate OTX-2002. We characterized OTX-2002 in HCC cell lines, measuring MYC mRNA and cell viability. OTX-2002 was tested for durable epigenetic and transcriptomic changes. Changes in MYC protein levels and pathway signaling were measured using proteomic methods. Finally, we analyzed activity of OTX-2002 in in vivo subcutaneous (subQ) and orthotopic HCC models by assessing tumor volume, tumor-associated bioluminescence (BLI) and immunohistochemistry (IHC). OTX-2002 was effective at decreasing MYC mRNA, protein and cell viability in HCC cells while sparing normal cells. In HCC cells, OTX-2002 median EC50 of inhibition is <0.001 ng/mL for MYC mRNA and 120 ng/mL for cell viability. Importantly, the effects of OTX-2002 persisted for >2 weeks, providing durable MYC mRNA repression. IV delivery of OTX-2002 in lipid nanoparticles at 3 and 6 mg/kg Q5D in a Hep 3B subQ model in athymic nude mice demonstrated statistically significant tumor growth inhibition (TGI) of 54% and 63%, respectively, by Day 23 compared to negative control. OTX-2002-treated mice did not have a significant decrease in bodyweight (BW) compared to negative control or sorafenib-treated mice. IHC of OTX-2002 and control treated tumors showed significant down-regulation of MYC with reduced proliferation (Ki67) and increased apoptosis (Caspase 3). In a Hep 3B orthotopic model 3 mg/kg OTX-2002 Q5D showed a comparable reduction of BLI to sorafenib at 50 mg/kg QD without the reduction in BW. Our findings identify a therapeutic in vitro and in vivo approach that enables transcriptional modulation of the MYC oncogene through precise epigenomic programming of the IGD in which it resides. Targeting MYC in this manner may represent a potentially differentiated and viable approach to the treatment of HCC in humans. Citation Format: William Senapedis, Elmer Figueroa, Kayleigh Gallagher, Jeremiah Farelli, Robert Lyng, Charles O'Donnell, Joseph Newman, Thomas McCauley. Epigenetic modulation of the MYC oncogene as a potential novel therapy for HCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2629.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.