Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity
Background: Maintenance of the genome is essential for cell survival, and impairment of the DNA damage response is associated with multiple pathologies including cancer and neurological abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical nonhomologous end-joining pa...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1276365/full |
| _version_ | 1827312369153343488 |
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| author | Sk Imran Ali Mohammad J. Najaf-Panah Kennedi B. Pyper F. Ester Lujan Johnny Sena Amanda K. Ashley |
| author_facet | Sk Imran Ali Mohammad J. Najaf-Panah Kennedi B. Pyper F. Ester Lujan Johnny Sena Amanda K. Ashley |
| author_sort | Sk Imran Ali |
| collection | DOAJ |
| description | Background: Maintenance of the genome is essential for cell survival, and impairment of the DNA damage response is associated with multiple pathologies including cancer and neurological abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical nonhomologous end-joining pathway, but it also has roles in modulating gene expression and thus, the overall cellular response to DNA damage.Methods: Using cells producing either wild-type (WT) or kinase-inactive (KR) DNA-PKcs, we assessed global alterations in gene expression in the absence or presence of DNA damage. We evaluated differential gene expression in untreated cells and observed differences in genes associated with cellular adhesion, cell cycle regulation, and inflammation-related pathways. Following exposure to etoposide, we compared how KR versus WT cells responded transcriptionally to DNA damage.Results: Downregulated genes were mostly involved in protein, sugar, and nucleic acid biosynthesis pathways in both genotypes, but enriched biological pathways were divergent, again with KR cells manifesting a more robust inflammatory response compared to WT cells. To determine what major transcriptional regulators are controlling the differences in gene expression noted, we used pathway analysis and found that many master regulators of histone modifications, proinflammatory pathways, cell cycle regulation, Wnt/β-catenin signaling, and cellular development and differentiation were impacted by DNA-PKcs status. Finally, we have used qPCR to validate selected genes among the differentially regulated pathways to validate RNA sequence data.Conclusion: Overall, our results indicate that DNA-PKcs, in a kinase-dependent fashion, decreases proinflammatory signaling following genotoxic insult. As multiple DNA-PK kinase inhibitors are in clinical trials as cancer therapeutics utilized in combination with DNA damaging agents, understanding the transcriptional response when DNA-PKcs cannot phosphorylate downstream targets will inform the overall patient response to combined treatment. |
| first_indexed | 2024-04-24T21:42:16Z |
| format | Article |
| id | doaj.art-19e3b32b6e184683acc3ecd9c8efe1c9 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-24T21:42:16Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-19e3b32b6e184683acc3ecd9c8efe1c92024-03-21T05:13:10ZengFrontiers Media S.A.Frontiers in Genetics1664-80212024-03-011510.3389/fgene.2024.12763651276365Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activitySk Imran Ali0Mohammad J. Najaf-Panah1Kennedi B. Pyper2F. Ester Lujan3Johnny Sena4Amanda K. Ashley5Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, United StatesDepartment of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, United StatesDepartment of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, United StatesDepartment of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, United StatesNational Center for Genome Resources, Santa Fe, NM, United StatesDepartment of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, United StatesBackground: Maintenance of the genome is essential for cell survival, and impairment of the DNA damage response is associated with multiple pathologies including cancer and neurological abnormalities. DNA-PKcs is a DNA repair protein and a core component of the classical nonhomologous end-joining pathway, but it also has roles in modulating gene expression and thus, the overall cellular response to DNA damage.Methods: Using cells producing either wild-type (WT) or kinase-inactive (KR) DNA-PKcs, we assessed global alterations in gene expression in the absence or presence of DNA damage. We evaluated differential gene expression in untreated cells and observed differences in genes associated with cellular adhesion, cell cycle regulation, and inflammation-related pathways. Following exposure to etoposide, we compared how KR versus WT cells responded transcriptionally to DNA damage.Results: Downregulated genes were mostly involved in protein, sugar, and nucleic acid biosynthesis pathways in both genotypes, but enriched biological pathways were divergent, again with KR cells manifesting a more robust inflammatory response compared to WT cells. To determine what major transcriptional regulators are controlling the differences in gene expression noted, we used pathway analysis and found that many master regulators of histone modifications, proinflammatory pathways, cell cycle regulation, Wnt/β-catenin signaling, and cellular development and differentiation were impacted by DNA-PKcs status. Finally, we have used qPCR to validate selected genes among the differentially regulated pathways to validate RNA sequence data.Conclusion: Overall, our results indicate that DNA-PKcs, in a kinase-dependent fashion, decreases proinflammatory signaling following genotoxic insult. As multiple DNA-PK kinase inhibitors are in clinical trials as cancer therapeutics utilized in combination with DNA damaging agents, understanding the transcriptional response when DNA-PKcs cannot phosphorylate downstream targets will inform the overall patient response to combined treatment.https://www.frontiersin.org/articles/10.3389/fgene.2024.1276365/fullDNA-PKcsDNA damage repairnon-homologous end-joiningetoposidegene expressiontranscriptome |
| spellingShingle | Sk Imran Ali Mohammad J. Najaf-Panah Kennedi B. Pyper F. Ester Lujan Johnny Sena Amanda K. Ashley Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity Frontiers in Genetics DNA-PKcs DNA damage repair non-homologous end-joining etoposide gene expression transcriptome |
| title | Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity |
| title_full | Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity |
| title_fullStr | Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity |
| title_full_unstemmed | Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity |
| title_short | Comparative analysis of basal and etoposide-induced alterations in gene expression by DNA-PKcs kinase activity |
| title_sort | comparative analysis of basal and etoposide induced alterations in gene expression by dna pkcs kinase activity |
| topic | DNA-PKcs DNA damage repair non-homologous end-joining etoposide gene expression transcriptome |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1276365/full |
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