Dataset Information

Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naive diffuse midline glioma models.

ABSTRACT:

Background

Diffuse midline gliomas (DMGs), including diffuse intrinsic pontine gliomas (DIPGs), have a dismal prognosis, with less than 2% surviving 5 years postdiagnosis. The majority of DIPGs and all DMGs harbor mutations altering the epigenetic regulatory histone tail (H3 K27M). Investigations addressing DMG epigenetics have identified a few promising drugs, including the HDAC inhibitor (HDACi) panobinostat. Here, we use clinically relevant DMG models to identify and validate other effective HDACi and their biomarkers of response.

Methods

HDAC inhibitors were tested across biopsy-derived treatment-naïve in vitro and in vivo DMG models with biologically relevant radiation resistance. RNA sequencing was performed to define and compare drug efficacy and to map predictive biomarkers of response.

Results

Quisinostat and romidepsin showed efficacy with low nanomolar half-maximal inhibitory concentration (IC50) values (~50 and ~5 nM, respectively). Comparative transcriptome analyses across quisinostat, romidepsin, and panobinostat showed a greater degree of shared biological effects between quisinostat and panobinostat, and less overlap with romidepsin. However, some transcriptional changes were consistent across all 3 drugs at similar biologically effective doses, such as overexpression of troponin T1 slow skeletal type (TNNT1) and downregulation of collagen type 20 alpha 1 chain (COL20A1), identifying these as potential vulnerabilities or on-target biomarkers in DMG. Quisinostat and romidepsin significantly (P < 0.0001) inhibited in vivo tumor growth.

Conclusions

Our data highlight the utility of treatment-naïve biopsy-derived models; establishes quisinostat and romidepsin as effective in vivo; illuminates potential mechanisms and/or biomarkers of DMG cell lethality due to HDAC inhibition; and emphasizes the need for brain tumor-penetrant versions of potentially efficacious agents.

SUBMITTER: Vitanza NA

PROVIDER: S-EPMC7992886 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Abstract Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer that is in need of urgent “outside the box” therapeutic approaches. Recent studies show that tumor cells adapt to stresses created by oncogenic mutations and these oncogene-induced adaptations create vulnerabilities that can be exploited to therapeutic ends. To uncover these oncogene-induced vulnerabilities in DMGs we conducted a genome-wide CRIPSR knockout screen in three DMG lines. The top common DMG dependency pathway that we discovered is de novo pyrimidine biosynthesis. Under normal conditions pyrimidine nucleotide needs are met through the salvage pathway. However, in DMG tumorigenesis, pyrimidine nucleotide synthesis is rewired such that the cells become dependent on the de novo biosynthesis pathway. De novo pyrimidine synthesis is catalyzed by CAD, DHODH and UMPS; all three genes are identified as dependencies in our screen and have been validated using shRNA mediated gene knockdown. Interestingly, DMG cells did not exhibit a dependency on the de novo purine biosynthesis pathway. Using a small molecule inhibitor of DHODH, BAY2402234 [currently studied in phase I trial for myeloid malignancies (NCT03404726)], we have demonstrated and validated, (i) efficacy and specificity of de novo pyrimidine synthesis inhibition in vitro in DMG cells; (ii) de novo pyrimidine addiction is not attributable to cell proliferation; (iii) DHODH inhibition induces apoptosis by hindering replication and inciting DNA damage; (iv) DHODH and ATR inhibition act synergistically to induce DMG cell death; and (v) critical in vivo efficacy. The in vivo experiment documents that BAY2402234 crosses the blood-brain barrier, is present in the brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in intracranial DMG tumors in mice, and prolongs survival of orthotopic DMG tumor bearing mice. Taken together, our studies have identified a novel metabolic vulnerability that can be translated for the treatment of DMG patients.

Project description:Diffuse midline glioma (DMG) is an aggressive pediatric tumor localized in the brainstem. The median survival after diagnosis is less than one year. Surgical resection is not possible due to the critical localization of the tumor and radiation therapy alone or in combination with chemotherapy show only minimal benefit. In 80% of cases, DIPGs are harbor genetic abnormalities such as a K27M mutation in histone H3, suggesting drugs targeting epigenetic anomalies might be efficient. Indeed, Grasso et al. (Nature Medicine, 2015) have shown that the histone deacetylase inhibitor panobinostat (PS) affects glioma cell growth in vitro and in vivo. PS is currently undergoing phase 1 clinical trials. To better understand the mechanism of action of PS on tumor cells, we performed a proteomic analysis by comparing DMG cells treated with panobinostat to control cells. We identified 2 proteins in PS-treated cells: EBP50 (or NHERF-1) and IRSp53 (or BAIAP2). EBP50 protein is implicated in invasion (Kislin et al. Neoplasia, 2009) but it can also act like a tumor suppressor on glioblastoma (Molina et al. Cancer Research, 2010). There is a dual role of the protein which depends on its localization in the cell: when localized at the cell membrane, EBP50 acts as a tumor suppressor, but has oncogenic properties when present in the cytoplasm or nucleus. Using electron microscopy combined with immunofluorescence, we could validate expression of EBP50 in all cellular compartments. IRSp53 is implicated in proliferation of tumor cells (Liu P.S. Oncogene, 2010) and may have an important role during migration and invasion (Funato et al., Cancer Research 2004). To elucidate the role of the two proteins in DIPG, we investigated effects of gene knockdown by siRNA and stable overexpression using lentiviruses. For each protein, we found a significant diminution of proliferation, migration and invasion and an increase in apoptosis cells were transfected with siRNAs. In contrast, overexpression of EBP50 did not have any effect on cells. Our results suggest that the two proteins induced by PS treatment are implicated in tumor progression and might constitute novel additional therapeutic targets, especially as adjuvant treatment together with PS.