Abstract 5331: Biological assessment of the virus-like drug conjugate AU-011 to specifically target a breadth of human cancer types

Introduction: AU-011 is a virus-like drug conjugate based on a human papillomavirus (HPV) derived virus-like particle (VLP) conjugated to a light-activated cytotoxic payload (IRDye700DX) currently in Phase II clinical trials for the treatment of primary choroidal melanoma. When activated by near-infrared light, AU-011 has a dual mechanism of action inducing rapid, tumor necrosis resulting in pro-immunogenic cell death and long-term anti-tumor immunity. HPV-derived VLPs bind a wide variety of tumor types via modified heparan sulfate proteoglycans (HSPG) found on the tumor surface. This study explores the breadth of tumor types that could benefit from a targeted treatment intervention with AU-011 and surveys genes and biological pathways that are positively and negatively associated with this targeting.

Methods: AU-011 binding, cytotoxicity and HSPG specificity was surveyed in 127 tumor cell lines representing breast, cervical, CNS (glioblastoma, astrocytoma), colon, esophageal, gastric, hematopoietic, lung, liver, melanoma (cutaneous or choroidal), oropharyngeal, ovarian, pancreas, prostate, renal, urothelial and skin cancers, and sarcomas (osteosarcomas, mesotheliomas, retinoblastomas). Publicly available gene expression data for 101 of these cell lines was cross-referenced to identify gene signatures that correlated (either positively or negatively) with AU-011 binding and cytotoxicity.

Results: AU-011 activity was observed for every tumor type examined, with some variation across several of the types. HSPG-specific binding was well-conserved across all tumor types tested except for most cells of lymphoid origin which are known to have HSPG deficiency. Collectively the tumor-derived cell lines exhibiting average binding EC50s < 100 pM were ocular cancers (choroidal melanomas and retinoblastomas) and solid tumors including urothelial, bone, breast, cervical, CNS, colon, cutaneous melanoma, esophageal, gastric, liver, lung, skin, oropharyngeal, ovarian, and renal. Urothelial, bone, breast, cervical, CNS, esophageal, gastric, liver, lung, melanoma, skin, ovarian, renal and retinoblastoma all exhibited AU-011 mediated cytotoxicity with an average potency of < 100pM. Correlative gene expression analysis demonstrated a strong association between AU-011 activity and genes involved in epithelial-to-mesenchymal transition, glycosaminoglycan biosynthesis/metabolism, and extracellular matrix interactions. Expression signatures for ribosomal activity and protein translation were negatively associated with AU-011 binding and activity.

Conclusions: Collectively these data demonstrate the wide potential applicability of AU-011 to target a number of tumor types, particularly those derived from neural or epithelial lineages. Importantly, a large portion of these tumors are accessible making their AU-011 targeting clinically translatable.

Citation Format: Rhonda C. Kines, Nathan R. Fons, Elisabet de los Pinos, John T. Schiller. Biological assessment of the virus-like drug conjugate AU-011 to specifically target a breadth of human cancer types [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 5331.

Hair follicle regeneration suppresses Ras-driven oncogenic growth

Healthy tissues can harbor cancer-associated mutations without developing tumors, yet the mechanisms behind this apparent tolerance are unclear. In this work, we demonstrate that the hair follicle skin epithelium uses regeneration as a means of suppressing Ras-driven oncogenic growth.

Mutations associated with tumor development in certain tissues can be nontumorigenic in others, yet the mechanisms underlying these different outcomes remains poorly understood. To address this, we targeted an activating Hras mutation to hair follicle stem cells and discovered that Hras mutant cells outcompete wild-type neighbors yet are integrated into clinically normal skin hair follicles. In contrast, targeting the Hras mutation to the upper noncycling region of the skin epithelium leads to benign outgrowths. Follicular Hras mutant cells autonomously and nonautonomously enhance regeneration, which directs mutant cells into continuous tissue cycling to promote integration rather than aberrancy. This follicular tolerance is maintained under additional challenges that promote tumorigenesis in the epidermis, including aging, injury, and a secondary mutation. Thus, the hair follicle possesses a unique, enhanced capacity to integrate and contain Hras mutant cells within both homeostatic and perturbed tissue, demonstrating that in the skin, multiple, distinct mechanisms exist to suppress oncogenic growth.

PPM1D mutations silence NAPRT gene expression and confer NAMPT inhibitor sensitivity in glioma

Pediatric high-grade gliomas are among the deadliest of childhood cancers due to limited knowledge of early driving events in their gliomagenesis and the lack of effective therapies available. In this study, we investigate the oncogenic role of PPM1D, a protein phosphatase often found truncated in pediatric gliomas such as DIPG, and uncover a synthetic lethal interaction between PPM1D mutations and nicotinamide phosphoribosyltransferase (NAMPT) inhibition. Specifically, we show that mutant PPM1D drives hypermethylation of CpG islands throughout the genome and promotes epigenetic silencing of nicotinic acid phosphoribosyltransferase (NAPRT), a key gene involved in NAD biosynthesis. Notably, PPM1D mutant cells are shown to be sensitive to NAMPT inhibitors in vitro and in vivo, within both engineered isogenic astrocytes and primary patient-derived model systems, suggesting the possible application of NAMPT inhibitors for the treatment of pediatric gliomas. Overall, our results reveal a promising approach for the targeting of PPM1D mutant tumors, and define a critical link between oncogenic driver mutations and NAD metabolism, which can be exploited for tumor-specific cell killing.

2-Hydroxyglutarate produced by neomorphic IDH mutations suppresses homologous recombination and induces PARP inhibitor sensitivity

2-Hydroxyglutarate (2HG) exists as two enantiomers, (R)-2HG and (S)-2HG, and both are implicated in tumor progression via their inhibitory effects on α-ketoglutarate (αKG)-dependent dioxygenases. The former is an oncometabolite that is induced by the neomorphic activity conferred by isocitrate dehydrogenase 1 (IDH1) and IDH2 mutations, whereas the latter is produced under pathologic processes such as hypoxia. We report that IDH1/2 mutations induce a homologous recombination (HR) defect that renders tumor cells exquisitely sensitive to poly(adenosine 5'-diphosphate-ribose) polymerase (PARP) inhibitors. This "BRCAness" phenotype of IDH mutant cells can be completely reversed by treatment with small-molecule inhibitors of the mutant IDH1 enzyme, and conversely, it can be entirely recapitulated by treatment with either of the 2HG enantiomers in cells with intact IDH1/2 proteins. We demonstrate mutant IDH1-dependent PARP inhibitor sensitivity in a range of clinically relevant models, including primary patient-derived glioma cells in culture and genetically matched tumor xenografts in vivo. These findings provide the basis for a possible therapeutic strategy exploiting the biological consequences of mutant IDH, rather than attempting to block 2HG production, by targeting the 2HG-dependent HR deficiency with PARP inhibition. Furthermore, our results uncover an unexpected link between oncometabolites, altered DNA repair, and genetic instability.

Abstract 2466: Development of a novel gene targeting and clone screening platform to engineer common pediatric glioma mutations into model cell lines

The utility of CRISPR/Cas9 gene targeting tools to alter endogenous genomic loci has revolutionized biomedical research across numerous disease focus areas, with especially large gains made in the development of disease models. However, the introduction of specific mutations using CRISPR/Cas9 can be associated with low yields of single cell clones harboring the desired homozygous or heterozygous mutations. Conventional clone screening methods can be a labor intensive and expensive process and thus, better approaches are needed to identify cells with the desired genotype(s). In parallel, there is a dearth of human tumor cell model systems for pediatric cancers, especially for Diffuse Intrinsic Pontine Glioma (DIPG). To address these needs, we recently designed and validated a platform which utilizes a novel, inducible Cas9 expression system coupled with a high-resolution DNA melt (HRM) analysis protocol to rapidly identify mutant clones. We applied our platform to model several common DIPG mutations, including truncating mutations within exon 6 of the gene, protein phosphatase 1D (PPM1D). Using our HRM analysis protocol, clones containing activating mutations in PPM1D were detectable and grouped distinctly from wild-type and non-functional clones; as validated through conventional Sanger sequencing and Ion Torrent Next Generation Sequencing. Importantly, multiple PPM1D mutant clones were generated in an expedited manner (< 4 weeks), using our unique HRM process-flow. We subsequently validated these clones in a collection of secondary assays, and we confirmed that the mutant proteins were functionally active. Several unique findings were identified in these studies, including substantial cell cycle-associated defects and basal activation of key proteins in the DNA damage response network. To our knowledge, we have created the first set of astrocyte cell lines harboring engineered PPM1D mutations at the endogenous gene locus. We are now testing these cell lines in high-throughput synthetic lethal screens to identify novel inhibitors of PPM1D-mutant DIPG tumors. These findings highlight the utility and power of our unique approach to rapidly create pertinent mutant cell lines for use in mutation-targeted biological assays. Our platform likely will become an invaluable tool for the development of better pediatric glioma cell line models in the future.

Citation Format: Nathan R. Fons, Yulia Surovtseva, Gregory A. Breuer, Ranjini K. Sundaram, Ranjit S. Bindra. Development of a novel gene targeting and clone screening platform to engineer common pediatric glioma mutations into model cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2466.

Abstract 4277: Development and validation of a novel IDH1-mutant astrocyte cell line as a model for high-grade gliomas

High-grade gliomas (HGGs) are devastating malignancies of the central nervous system, and few treatment options are available for these tumors. In the most malignant form of the disease, glioblastoma multiforme (GBM), over 90% of patients will succumb to their tumor within 5 years after standard of care treatment, consisting of surgery, radiation therapy, and temozolomide chemotherapy. It is now clear that gliomas are molecularly heterogeneous entities, with mutations in tumor suppressors and oncogenes defining many distinct sub-types with important therapy implications. However, almost all HGGs are treated with a limited array of initial therapies, regardless of these molecular differences. Isocitrate dehydrogenase-1 (IDH1), a gene recently found to be mutated in many gliomas, is involved in the conversion of isocitrate to 2-oxoglutarate in cells. The IDH1 R132H mutant enzyme converts 2-oxoglutarate to the oncometabolite (R)-2-hydroxyglutarate (D2HG), which leads to profound metabolic alterations in tumor cells. In addition, recent studies indicate that mutations in IDH1 may also induce altered DSB repair, differential sensitivities to chemo-radiotherapy, and substantial changes in chromatin modifications. Here, we present the creation of a novel astrocyte cell line harboring an engineered heterozygous IDH1 R132H mutation at the endogenous gene locus using CRISPR/Cas9 gene editing. We confirmed expression of the engineered mutation at the protein level, and we have characterized this cell line in a comprehensive panel of functional assays. In particular, we demonstrated that our mutant cell clones secrete high levels of D2HG, and we confirmed that the levels of this oncometabolite can be suppressed with small molecule inhibitors of mutant IDH1. We also characterized the DNA damage response network in IDH1-mutant cells using high-content DNA damage foci assays recently developed by our group, and also in clonogenic survival assays. To our knowledge, this is the first report of an astrocyte cell line harboring an engineered, heterozygous R132H mutation at the endogenous locus. This novel cell line represents a new model system for studying gliomas and has tremendous applications for further cell characterization, mechanistic studies, and drug screening.

Citation Format: Nathaniel D. Robinson, Karin R. Purshouse, Nathan R. Fons, Gregory A. Breuer, Stefan Pusch, Andreas von Deimling, Ranjini K. Sundaram, Ranjit S. Bindra. Development and validation of a novel IDH1-mutant astrocyte cell line as a model for high-grade gliomas. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4277.