DDDR-78. Identifying common transcriptional mechanisms in treatment-resistant glioma

Abstract BACKGROUND Glioma, the most common primary brain tumor, shows poor prognosis and resistance to first-line therapies, like temozolomide (TMZ), lomustine (LOM) and panobinostat-marizomib (PM), complicating treatment and diminishing disease-free survival. It is critical to investigate the molecular mechanisms that underlie chemoresistance to develop effective therapies. This study examines common transcriptional networks that facilitate chemoresistance to identify novel therapeutic targets that may overcome resistance. METHODS The pediatric high-grade glioma KNS42 cell line was chronically treated with increasing doses of TMZ, LOM, or PM to induce drug resistance (RES); control cells received vehicle (DMSO) treatment. Bulk-RNA sequencing was performed followed by differential gene expression analyses (PartekFlow-ANOVA/DESeq2) followed by pathway and comparison analysis (QIAGEN IPA, |FDR|<0.05). RESULTS RNA-sequencing analysis followed by comparison-analysis revealed differential gene expression in treatment-resistant glioma cells as compared to control cells, including 3,839 differentially expressed genes (DEGs) in LOM RES, 3,641 in TMZ RES, and 3,445 in PM RES groups compared to control group. Among these, 374, 417, and 360 DEGs were downregulated in LOM, TMZ, and PM RES cells, respectively, while 265 (LOM and TMZ RES) and 216 (PM RES) DEGs were upregulated (log2FC > 2; p < 0.05). Interestingly, when the top 10 upregulated genes from each resistant group were compared, six genes (VCAN, FOXA1, SOX2, PDGFRA, ERBB4, and COL4A) were found to be commonly upregulated in all 3 resistant groups. We further confirmed that SOX2, PDGFRA, and ERBB4 are upregulated at the protein level. Ongoing studies will test whether these 6 DEGs are required for mediating resistance against diverse drugs. CONCLUSION RNA-sequencing identified common genes linked to TMZ, LOM, and PM chemoresistance, revealing key genetic networks involved in acquiring and maintaining drug resistance. Targeting these pathways, along with epigenetic silencing and/or combinatorial therapies, may resensitize chemoresistant cells and allow for effective treatment of glioma.