Journal Article

Detection of gene mutations and gene–gene fusions in circulating cell‐free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis

Har‐Nof, Sagi, Levy‐Barda, Adva, Gorohovski, Alessandro, Palande, Vikrant, Perez, Shira, Glass, Rainer, Detroja, Rajesh, Kanner, Andrew A., Raviv Shay, Dorith, Laviv, Yoseph, Viviana Karpuj, Marcela, Siegal, Tali, Kurtz, Marina, Frenkel‐Morgenstern, Milana, Flueh, Charlotte

2022

Overview

Glioblastoma (GBM) is the most common type of glioma and is uniformly fatal. Currently, tumour heterogeneity and mutation acquisition are major impedances for tailoring personalized therapy. We collected blood and tumour tissue samples from 25 GBM patients and 25 blood samples from healthy controls. Cell‐free DNA (cfDNA) was extracted from the plasma of GBM patients and from healthy controls. Tumour DNA was extracted from fresh tumour samples. Extracted DNA was sequenced using a whole‐genome sequencing procedure. We also collected 180 tumour DNA datasets from GBM patients publicly available at the TCGA/PANCANCER project. These data were analysed for mutations and gene–gene fusions that could be potential druggable targets. We found that plasma cfDNA concentrations in GBM patients were significantly elevated (22.6 ± 5 ng·mL−1), as compared to healthy controls (1.4 ± 0.4 ng·mL−1) of the same average age. We identified unique mutations in the cfDNA and tumour DNA of each GBM patient, including some of the most frequently mutated genes in GBM according to the COSMIC database (TP53, 18.75%; EGFR, 37.5%; NF1, 12.5%; LRP1B, 25%; IRS4, 25%). Using our gene–gene fusion database, ChiTaRS 5.0, we identified gene–gene fusions in cfDNA and tumour DNA, such as KDR–PDGFRA and NCDN–PDGFRA, which correspond to previously reported alterations of PDGFRA in GBM (44% of all samples). Interestingly, the PDGFRA protein fusions can be targeted by tyrosine kinase inhibitors such as imatinib, sunitinib, and sorafenib. Moreover, we identified BCR–ABL1 (in 8% of patients), COL1A1–PDGFB (8%), NIN–PDGFRB (8%), and FGFR1–BCR (4%) in cfDNA of patients, which can be targeted by analogues of imatinib. ROS1 fusions (CEP85L–ROS1 and GOPC–ROS1), identified in 8% of patient cfDNA, might be targeted by crizotinib, entrectinib, or larotrectinib. Thus, our study suggests that integrated analysis of cfDNA plasma concentration, gene mutations, and gene–gene fusions can serve as a diagnostic modality for distinguishing GBM patients who may benefit from targeted therapy. These results open new avenues for precision medicine in GBM, using noninvasive liquid biopsy diagnostics to assess personalized patient profiles. Moreover, repeated detection of druggable targets over the course of the disease may provide real‐time information on the evolving molecular landscape of the tumour. Personalized therapy of patients with glioblastoma (GBM) is challenging owing to tumour heterogeneity. Here, we extracted and sequenced cell‐free DNA (cfDNA) from the plasma of 25 GBM patients and tumour DNA from fresh tumour samples. We found that cfDNA concentrations in the plasma of GBM patients were significantly elevated, as compared to healthy controls. Moreover, we identified unique mutations and gene–gene fusions in the cfDNA and tumour DNA of GBM patients, some of which could be therapeutically targeted by tyrosine kinase inhibitors.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc,Wiley
• Subject: Antimitotic agents / Antineoplastic agents / Apoptosis / Biopsy / Brain cancer / Cancer therapies / circulating cell‐free DNA / Collagen (type I) / Deoxyribonucleic acid / DNA / druggable / Ethylenediaminetetraacetic acid / Fibroblast growth factor receptor 1 / Gene fusion / gene mutation / Gene mutations / Genes / Genetic aspects / gene‐gene fusion / Genomes / Glioblastoma / Glioma / Imatinib / Leukemia / liquid biopsy / Magnetic resonance imaging / Medical prognosis / Medical research / Medicine, Experimental / Mutation / Nucleotide sequence / p53 Protein / Patients / Plasma / Platelet-derived growth factor / Precision medicine / Protein-tyrosine kinase / Tumor proteins / Tumors / Whole genome sequencing