RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target
Glioblastoma (GBM) is an aggressive brain cancer with a median survival time of 14.6 months after diagnosis. GBM cells have altered metabolism and exhibit the Warburg effect, preferentially producing lactate under aerobic conditions. After standard-of-care treatment for GBM, there is an almost 100%...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/841 |
| _version_ | 1797605283590045696 |
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| author | Brian E. White Yichuan Liu Hakon Hakonarson Russell J. Buono |
| author_facet | Brian E. White Yichuan Liu Hakon Hakonarson Russell J. Buono |
| author_sort | Brian E. White |
| collection | DOAJ |
| description | Glioblastoma (GBM) is an aggressive brain cancer with a median survival time of 14.6 months after diagnosis. GBM cells have altered metabolism and exhibit the Warburg effect, preferentially producing lactate under aerobic conditions. After standard-of-care treatment for GBM, there is an almost 100% recurrence rate. Hypoxia-adapted, treatment-resistant GBM stem-like cells are thought to drive this high recurrence rate. We used human T98G GBM cells as a model to identify differential gene expression induced by hypoxia and to search for potential therapeutic targets of hypoxia adapted GBM cells. RNA sequencing (RNAseq) and bioinformatics were used to identify differentially expressed genes (DEGs) and cellular pathways affected by hypoxia. We also examined expression of lactate dehydrogenase (<i>LDH</i>) genes using qRT-PCR and zymography as <i>LDH</i> dysregulation is a feature of many cancers. We found 2630 DEGs significantly altered by hypoxia (p < 0.05), 1241 upregulated in hypoxia and 1389 upregulated in normoxia. Hypoxia DEGs were highest in pathways related to glycolysis, hypoxia response, cell adhesion and notably the endoplasmic reticulum, including the inositol-requiring enzyme 1 (IRE1)-mediated unfolded protein response (UPR). These results, paired with numerous published preclinical data, provide additional evidence that inhibition of the IRE1-mediated UPR may have therapeutic potential in treating GBM. We propose a possible drug repurposing strategy to simultaneously target IRE1 and the spleen tyrosine kinase (SYK) in patients with GBM. |
| first_indexed | 2024-03-11T04:58:51Z |
| format | Article |
| id | doaj.art-3e8031397a9c4a5cbbf2ab75e0bedf8a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:58:51Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-3e8031397a9c4a5cbbf2ab75e0bedf8a2023-11-17T19:23:17ZengMDPI AGGenes2073-44252023-03-0114484110.3390/genes14040841RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic TargetBrian E. White0Yichuan Liu1Hakon Hakonarson2Russell J. Buono3Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USACenter for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USACenter for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USADepartment of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USAGlioblastoma (GBM) is an aggressive brain cancer with a median survival time of 14.6 months after diagnosis. GBM cells have altered metabolism and exhibit the Warburg effect, preferentially producing lactate under aerobic conditions. After standard-of-care treatment for GBM, there is an almost 100% recurrence rate. Hypoxia-adapted, treatment-resistant GBM stem-like cells are thought to drive this high recurrence rate. We used human T98G GBM cells as a model to identify differential gene expression induced by hypoxia and to search for potential therapeutic targets of hypoxia adapted GBM cells. RNA sequencing (RNAseq) and bioinformatics were used to identify differentially expressed genes (DEGs) and cellular pathways affected by hypoxia. We also examined expression of lactate dehydrogenase (<i>LDH</i>) genes using qRT-PCR and zymography as <i>LDH</i> dysregulation is a feature of many cancers. We found 2630 DEGs significantly altered by hypoxia (p < 0.05), 1241 upregulated in hypoxia and 1389 upregulated in normoxia. Hypoxia DEGs were highest in pathways related to glycolysis, hypoxia response, cell adhesion and notably the endoplasmic reticulum, including the inositol-requiring enzyme 1 (IRE1)-mediated unfolded protein response (UPR). These results, paired with numerous published preclinical data, provide additional evidence that inhibition of the IRE1-mediated UPR may have therapeutic potential in treating GBM. We propose a possible drug repurposing strategy to simultaneously target IRE1 and the spleen tyrosine kinase (SYK) in patients with GBM.https://www.mdpi.com/2073-4425/14/4/841glioblastomaLDHRNA sequencingIRE1hypoxiaT98G |
| spellingShingle | Brian E. White Yichuan Liu Hakon Hakonarson Russell J. Buono RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target Genes glioblastoma LDH RNA sequencing IRE1 hypoxia T98G |
| title | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target |
| title_full | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target |
| title_fullStr | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target |
| title_full_unstemmed | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target |
| title_short | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target |
| title_sort | rna sequencing in hypoxia adapted t98g glioblastoma cells provides supportive evidence for ire1 as a potential therapeutic target |
| topic | glioblastoma LDH RNA sequencing IRE1 hypoxia T98G |
| url | https://www.mdpi.com/2073-4425/14/4/841 |
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