Targeting DNA Repair for Cancer Therapy.

Yale University, New Haven CT

Investigators

Linked publications & trials

Abstract

This R35 renewal application seeks to identify and exploit tumor-specific vulnerabilities based on DNA repair deficiencies and to develop novel therapeutic strategies that specifically target tumors. In the recent funding period, we discovered that elevated levels of the oncometabolites 2-hydroxyglutarate (2HG), fumarate, and succinate in human cancers inhibit homology-dependent repair (HDR) by disrupting chromatin signaling at DNA double strand breaks (DSBs), conferring a previously unsuspected vulnerability to PARP inhibitors (PARPi). These oncometabolites are over-produced in human malignancies with mutations in isocitrate dehydrogenase- 1 and -2 (IDH1/2), fumarate hydratase (FH), and succinate dehydrogenase (SDH). Our work, published in Nature, Nature Genetics, and Science Translational Medicine, has led to seven new clinical trials testing a new therapeutic paradigm of treating these tumors with PARPi, with promising initial results. In this renewal, we propose to further elucidate fundamental mechanisms underlying the DNA repair deficiency in oncometabolite- producing cells, with a focus on chromatin remodelers and DNA end-protection factors, prompted by new data from RNA-sequencing analyses. We will also probe potential pathways of PARPi resistance and develop strategies to overcome them. Approaches will include comprehensive analyses of DNA repair and chromatin regulation, unbiased CRISPR screens, and small molecule drug screens. We have also demonstrated tumor-specific targeting by peptide-drug conjugates via a pH-sensitive peptide (pHLIP) that exploits tumor acidity, with a pHLIP-exatecan conjugate that we developed now in a Phase 1 trial. Based on our pre-clinical work that established specific delivery to tumors with sparing of bone marrow, we propose to develop new pHLIP-small molecule conjugates that inhibit the DNA repair factor, DNA-PK, to selectively radiosensitize tumors while sparing healthy tissue. We will perform tumor efficacy and normal tissue toxicity studies with a goal of advancing a tumor-specific radiosensitizing agent for clinical translation. We have also produced a novel version of our cell-penetrating and tumor targeting antibody (designated V66, a humanized 3E10 variant). With this antibody, we will test a new hypothesis that we can exploit intracellular antibody/antigen clearance pathways to develop bispecific antibodies as selective protein degraders, combining a V66 arm (for its tumor targeting and cell penetration properties) with a second antibody arm specific for binding to an intracellular factor. This work could provide a new class of cell-penetrating, proteolysis targeting antibodies (PROTABs) to degrade otherwise undruggable intracellular factors for cancer therapy. Importantly, we have now obtained key proof-of-concept data that we can achieve targeted protein degradation of GFP by treatment of cells with a newly generated V66/anti-GFP bispecific antibody. This work spans from foundational basic science to pre-clinical animal tumor work, with potential for clinical translation, and so is well suited to the broader scope of the R35 funding mechanism.