Druggable genomic landscapes of high-grade gliomas

Abstract

Background: Despite the putatively targetable genomic landscape of high-grade gliomas, the long-term survival benefit of genomically-tailored targeted therapies remains discouraging.

Methods: Using glioblastoma (GBM) as a representative example of high-grade gliomas, we evaluated the clonal architecture and distribution of hotspot mutations in 388 GBMs from the Cancer Genome Atlas (TCGA). Mutations were matched with 54 targeted therapies, followed by a comprehensive evaluation of drug biochemical properties in reference to the drug's clinical efficacy in high-grade gliomas. We then assessed clinical outcomes of a cohort of patients with high-grade gliomas with targetable mutations reviewed at the Johns Hopkins Molecular Tumor Board (JH MTB; n = 50).

Results: Among 1,156 sequence alterations evaluated, 28.6% represented hotspots. While the frequency of hotspot mutations in GBM was comparable to cancer types with actionable hotspot alterations, GBMs harbored a higher fraction of subclonal mutations that affected hotspots (7.0%), compared to breast cancer (4.9%), lung cancer (4.4%), and melanoma (1.4%). In investigating the biochemical features of targeted therapies paired with recurring alterations, we identified a trend toward higher lipid solubility and lower IC₅₀ in GBM cell lines among drugs with clinical efficacy. The drugs' half-life, molecular weight, surface area and binding to efflux transporters were not associated with clinical efficacy. Among the JH MTB cohort of patients with IDH1 wild-type high-grade gliomas who received targeted therapies, trametinib monotherapy or in combination with dabrafenib conferred radiographic partial response in 75% of patients harboring BRAF or NF1 actionable mutations. Cabozantinib conferred radiographic partial response in two patients harboring a MET and a PDGFRA/KDR amplification. Patients with IDH1 wild-type gliomas that harbored actionable alterations who received genotype-matched targeted therapy had longer progression-free (PFS) and overall survival (OS; 7.37 and 14.72 respectively) than patients whose actionable alterations were not targeted (2.83 and 4.2 months respectively).

Conclusion: While multiple host, tumor and drug-related features may limit the delivery and efficacy of targeted therapies for patients with high-grade gliomas, genotype-matched targeted therapies confer favorable clinical outcomes. Further studies are needed to generate more data on the impact of biochemical features of targeted therapies on their clinical efficacy for high-grade gliomas.

Keywords: actionable mutation; genomic landscape; glioblastoma; glioma; molecular tumor board; precision oncology; targeted therapies.

Figure 1

Genomic heterogeneity of glioblastomas and distribution of recurring mutations within cancer hallmarks and gene pathways. (A) Illustrates the genomic landscape and clonal composition of the 329 GBMs in the TCGA cohort with clonality assessments. 65.9% of tumors harbored a hotspot sequence alteration, and 46.2% harbored at least one targetable alteration depicted in green. The number of nonsynonymous mutations within each of the five most altered signaling pathways is illustrated; red represents two or more mutations occurring within signaling pathways/cancer hallmarks, orange represents the occurrence of one mutation, and light yellow represents no mutation. Genomic alterations in GBM tumors frequently occur in genes within core signaling pathways and cancer hallmarks. (B) Further illustrates the hotspot and sub-clonal genomic alterations within the five altered core signaling pathways. The bar plot represents the number of mutations observed in all the GBMs (n = 388) that we evaluated from the TCGA. A sizable fraction of hotspot sequence alterations (28.6%) is observed in GBM. Among alterations with clonality assessments, 84.7% were clonal mutations. The distribution of hotspot clonal mutations in GBM within each gene is represented in light purple, sub-clonal hotspot mutations are shown in light orange, sub-clonal non-hotspot mutations are illustrated in dark orange and clonal non-hotspot mutations are illustrated in dark purple. All remaining non-synonymous alterations are represented in green.

Figure 2

Overview of factors that conceptually affect the efficacy of genotype-matched targeted therapies in brain tumors. (A) Illustration of several features that may limit the accumulation of targeted therapies in the brain and their clinical efficacy. The integrity of the blood-brain barrier (BBB) may be compromised in primary brain tumors, allowing drugs to cross into the tumor irrespective of their biochemical properties. The BBB represents the intact barrier composed of endothelial cells, pericytes, and astrocytes that is present in non-enhancing brain regions. The tight junctions at the blood–brain barrier and efflux transporters such as (ABCB1 and ABCG2) limit the ability of drugs to permeate an intact blood–brain barrier. Other biochemical features, such as the drugs’ surface area, lipophilicity, and reversible binding, can also affect the ability of those drugs to concentrate in the brain. Drugs with a small surface area, elevated lipid solubility, and irreversible binding require a lower IC₅₀ to adequately inhibit their target on tumor cells. The opposite holds true for drugs with a large surface area, low lipid solubility, and reversible binding. (B) Illustration of the most commonly altered signaling pathways observed in GBM, a representative example of high-grade glioma, based on the TCGA data. The PI3K/AKT/mTOR and RAS/Raf/MAPK pathways are frequently altered and conceptually represent a viable therapeutic target. Alterations within cell cycle regulating genes, such as, in MDM2, MDM4, CKDN2A/B, and CDK4/6 are actionable. Chromatin regulation can be targeted through IDH1, ARID1A, and EZH2 targeted therapies. Alterations in DNA damage repair are exemplified by targetable BRCA1/2 mutations.

Figure 3

Heatmap showing the biochemical features of 54 genotype-targeted therapies. This figure illustrates the different biochemical features of 54 targeted therapies against the most commonly occurring genomic alterations (≥1%) in GBM, among which the molecular weight, surface area, lipid solubility, charge, half-maximal inhibitory concentration, drugs’ reversible binding to their target, their half-life, and their binding to efflux transporters at the blood brain barrier. The brain-to-blood ratio and the maximal plasma and brain (tumor/non-tumor) concentrations obtained from preclinical studies as well as maximum tolerated dose (MTD), dose frequency and clinical efficacy of drugs are also displayed here. For clinical efficacy, light colors reflect weak evidence from phase 1 trials and case reports/series whereas darker shades of color reflect strong evidence from phase 2 trials. The highest level of evidence for each targeted therapy is also provided in the heatmap. The CDK4/6 inhibitor abemaciclib, the receptor tyrosine kinase (RTK) inhibitor cabozantanib, the BRAF inhibitors dabrafenib and vemurafenib, the FGFR inhibitor infigratinib and the MEK inhibitors selumetinib and trametinib have strong evidence suggesting clinical efficacy. The PARP inhibitors talazoparib, olaparib, and pamiparib, the EGFR inhibitor osimertinib, the ERK inhibitor ulixertinib, the FGFR inhibitor erdafitinib, the IDH inhibitors ivosidenib and vorasidenib, the MEK inhibitors binimetinib and cobimetinib, the NTRK inhibitor larotrectinib, the ROS1 inhibitor lorlatinib and the ROS1/NTRK inhibitor entrectinib have weak evidence suggesting clinical efficacy. Dabrafenib and vemurafenib both have an elevated lipid solubility, vemurafenib also has a small surface area and a long half-life while dabrafenib has a low IC₅₀. Aside from the low molecular weight and surface area that is common to all PARP inhibitors, olaparib, talazoparib, and pamiparib also have a longer half-life than veliparib that was shown to have no clinical efficacy in phase 2 trials. Veliparib also has an elevated IC₅₀ in GBM-specific cell lines. Abemaciclib, the CDK4/6 inhibitor with the highest lipid solubility and lowest surface area is the only drug with clinical efficacy in this class. Cabozantinib has a higher lipid solubility, lower surface area and lower IC₅₀ than other RTK inhibitors and is the only one that was shown to have clinical efficacy. Osimertinib irreversibly binds to EGFR, has a high lipid solubility, small surface area, long half-life, and elevated maximal brain (tumor and non-tumor) concentrations. MW, molecular weight; IC₅₀, half-maximal inhibitory concentration; Cmax, maximal concentration; MTD, maximal tolerated dose, *in preclinical studies.

Figure 4

Clinical outcomes of patients with primary brain tumors harboring targetable alterations reviewed at the Johns Hopkins Molecular Tumor Board. This figure illustrates the survival outcomes (PFS and OS) of 18 patients with high-grade gliomas, treated with targeted agents after review and following targeted therapy recommendations at the Johns Hopkins MTB. The solid bar plot illustrates the duration of treatment in months, while bar colors correspond to the targeted drug administered. Overall survival is presented by a dotted line; death is illustrated with an X, and loss to follow up is presented with an * at the end of the survival line. Two patients had an IDH1 mutant tumor; one was treated with ivosedinib and the other with cabozantanib for a MET/KIT amplification. Among the patients with IDH wild-type tumors, eight patients had radiographic partial response to the targeted therapy they received; four of them had received trametinib targeting an NF1 alteration, two had received trametinib and dabrafenib targeting a BRAF V600E alteration and the last two had received cabozantinib targeting a MET amplification in one tumor and a PDGFRA/KDR amplification in the other. Two patients with tumors harboring an NF1 alteration had radiographic stable disease on trametinib. Four patients with PDGFRA amplification, wild-type TP53, BRCA1, and BRCA2 alterations had progressive disease as best radiographic response to targeted therapy and two patients with EGFR and CDK4 amplification were lost to follow up before radiographic response could be assessed.