Transcriptome analysis of glioblastoma multiforma patients

Glioblastoma (GBM) is the most common and aggressive brain tumor malignancy with an average survival of approximately 12 months. Viruses like human cytomegalovirus, ionizing radiation, occupational exposure to rubber and petrochemical materials are associated with increased risk. To gain deeper insights into the molecular processes involved we aimed to detect differentially expressed genes in GBM. Fresh paired normal and tumor tissue samples were obtained from patients. Immunostaining was performed to validate the nature of both tissue groups. After RNA extraction and reverse transcription, we prepared libraries for 12 pairs of tumors. Emulsion PCR and were sequencing were performed. qRT PCR was performed in 26 tissue pairs for verification. Three of 12 pairs were excluded as a result of the PCA, as normal tissue from these patients showed tumor-like characteristics. 3,062 differentially expressed genes (p<0.001). Detection of the most significant pathways, upstream regulators and target genes in glioblastoma was done by IPA. A total 54 genes were selected as candidates for their possible role in tumor development or technical validation and analyzed in 26 pairs. The results of RT PCR were in agreement with NGS using Pearson Correlation. The pathways displaying most frequent changes were the Axonal Guidance Signaling, GABA and Glutamat receptor signaling pathways. Expression of known factors involved in glioblastoma formation as upstream regulators, such as ANXA2, TGFB1 and NUPR1. Besides these, DMBX1 and FAM180A were overexpressed and KCNV1 was downexpressed target genes in glioblastoma, which are not previously shown. We suggest that the genes detected in this study may provide candidate biomarkers in glioblastoma which warrants further investigation by functional tests. Key Words: Glioblastoma, RNAseq, upstream regulators, TGFB1, FAM180A.