ena-STUDY-KOC UNIVERSITY-04-07-2020-14:33:25:032-1307
Oncopanel testing capture was carried out with Illumina's TruSight Cancer Kit, which screens 94 genes and 284SNPs (Illumina, Inc). Sequencing was performed using MiSeq sequencer (Illumina) to produce 2 × 150 bp reads. Raw reads were mapped against reference genome hg19 using bwa-mem, de-duplicated using Picard tools and variant calling was performed using GATK best practices pipeline. Quality filtered variants (minimum of × 20 coverage and no more than 10% MAPQ0) were annotated using ANNOVAR with avSNP release of 142, 1000 genomes release of 2014 along with NIH-NHLBI 6500 exome database version 2. MAF filter (<0.01) was set based on ExAC, NIH 6500, gnomAD and 1000 genomes data. Pathogenicity evaluation was performed based on the inheritance mode, database entries (HGMD, ClinVar, CentoMD), in silico prediction tools (SIFT, Polyphen2, MutationTaster) and ACMG recommendations. All intronic variants located outside the boundaries of 10 bp from the exons and synonymous exonic ones were filtered out. Putative splicing variants were analyzed using Human Splicing Finder (HSF).
Glioblastoma is a malignant brain cancer with limited treatment options and high mortality rate.  While established Glioblastoma cell line models provide valuable information, they ultimately lose most primary characteristics of tumors under long-term serum culture conditions. Therefore, established cell lines do not necessarily recapitulate genetic and morphological characteristics of real tumors. In this study, in line with the growing interest in using primary cell line models derived from patient tissue, we generated a primary glioblastoma cell line, KUGBM8 and characterized its genetic alterations, long term growth ability, tumor formation capacity and its response to Temozolomide, the front-line chemotherapy utilized clinically.  In addition, we performed a drug repurposing screen on the KUGBM8 cell line to identify FDA-approved agents that can be incorporated into Glioblastoma treatment regimen and identified Topotecan as a lead drug among 1200 drugs. We showed Topotecan can induce cell death in KUGBM8 and other primary cell lines and cooperate with Temozolomide in low dosage combinations. Together, our study provides a new primary cell line model that can be suitable for both in vitro and in vivo studies and suggests that Topotecan can offer promise as a therapeutic approach for glioblastoma.
Glioblastoma is a malignant brain cancer with limited treatment options and high mortality rate.  While established Glioblastoma cell line models provide valuable information, they ultimately lose most primary characteristics of tumors under long-term serum culture conditions. Therefore, established cell lines do not necessarily recapitulate genetic and morphological characteristics of real tumors. In this study, in line with the growing interest in using primary cell line models derived from patient tissue, we generated a primary glioblastoma cell line, KUGBM8 and characterized its genetic alterations, long term growth ability, tumor formation capacity and its response to Temozolomide, the front-line chemotherapy utilized clinically.  In addition, we performed a drug repurposing screen on the KUGBM8 cell line to identify FDA-approved agents that can be incorporated into Glioblastoma treatment regimen and identified Topotecan as a lead drug among 1200 drugs. We showed Topotecan can induce cell death in KUGBM8 and other primary cell lines and cooperate with Temozolomide in low dosage combinations. Together, our study provides a new primary cell line model that can be suitable for both in vitro and in vivo studies and suggests that Topotecan can offer promise as a therapeutic approach for glioblastoma.