Drug repurposing using transcriptome sequencing and virtual drug screening in a patient with glioblastoma

Mohamed E M Saeed,Frederik Wenz,Henry Johannes Greten,Frank A Giordano,Onat Kadioglu,Adem Yildirim,Thomas Efferth,Katharina Mayr

doi:10.1007/s10637-020-01037-7

Abstract

SummaryBackground Precision medicine and drug repurposing are attractive strategies, especially for tumors with worse prognosis. Glioblastoma is a highly malignant brain tumor with limited treatment options and short survival times. We identified novel BRAF (47-438del) and PIK3R1 (G376R) mutations in a glioblastoma patient by RNA-sequencing. Methods The protein expression of BRAF and PIK3R1 as well as the lack of EGFR expression as analyzed by immunohistochemistry corroborated RNA-sequencing data. The expression of additional markers (AKT, SRC, mTOR, NF-κB, Ki-67) emphasized the aggressiveness of the tumor. Then, we screened a chemical library of > 1500 FDA-approved drugs and > 25,000 novel compounds in the ZINC database to find established drugs targeting BRAF47-438del and PIK3R1-G376R mutated proteins. Results Several compounds (including anthracyclines) bound with higher affinities than the control drugs (sorafenib and vemurafenib for BRAF and PI-103 and LY-294,002 for PIK3R1). Subsequent cytotoxicity analyses showed that anthracyclines might be suitable drug candidates. Aclarubicin revealed higher cytotoxicity than both sorafenib and vemurafenib, whereas idarubicin and daunorubicin revealed higher cytotoxicity than LY-294,002. Liposomal formulations of anthracyclines may be suitable to cross the blood brain barrier. Conclusions In conclusion, we identified novel small molecules via a drug repurposing approach that could be effectively used for personalized glioblastoma therapy especially for patients carrying BRAF47-438del and PIK3R1-G376R mutations.

Highlights

Half of the brain tumors represent diffuse gliomas, and the World Health Organization (WHO) provided classificationUniversity of Mainz, Mainz, Germany 4 University Hospital Freiburg, Freiburg im Breisgau, Germany 5 Department of Radiation Oncology, University Hospital Bonn, Bonn, Germany criteria to predict the clinical behavior of these neoplasms [1]
Various genetic mutations and aberration have been identified in glioblastoma patients, such as O-6-methylguanine-DNA methyltransferase (MGMT) methylation [3, 4], BRAFG596A [5], BRAFV600E [5,6,7], PIK3R1G376R, PIK3R1D560Y, PIK3R1N564K mutations [8]
Specific mutations have been identified in B-Raf proto-oncogene (BRAF) (BRAF47-438del, BRAF-TTYH3 fusion), Phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), MAP3K4, MAP3K5, and Protein tyrosine kinase 2 (PTK2)

Summary

Introduction

Glioblastoma is classified as grade IV/IV gliomas with specific characteristics, including high cellularity, cellular pleomorphism, nuclear atypia and necrosis [2]. Various genetic mutations and aberration have been identified in glioblastoma patients, such as MGMT methylation [3, 4], BRAFG596A [5], BRAFV600E [5,6,7], PIK3R1G376R, PIK3R1D560Y, PIK3R1N564K mutations [8]. The demand for effective novel agents to combat cancer has drawn the attention to specific molecular alterations in cancer cells as targets for therapy [9]. The concept of precision medicine implies the application of targeted drugs coupled with specific diagnostic assays in order to determine whether patients are likely to benefit from targeted therapy.

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Conclusion