Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Cell Line Maintenance and Differentiation
2.2. BTZ Dose Determination
2.3. Experimental Design
2.4. DNA Extraction
2.5. Genome-Wide Methylation Analyses
2.6. Identification of Methylation Changes Attributed to BTZ Treatment
2.7. Functional Analysis
2.8. High-Dimensional Data Visualization
2.9. Statistical Analysis
2.10. Validation of Identified CpGs in Independent Experiment Data
3. Results
3.1. Long-Term Culture of dLUHMES Cells Does Not Affect Methylation Status of the Vast Majority of CpG Sites Targeted by EPIC Array
3.2. Globally Bortezomib Treatment Induces Hypomethylation in dLUHMES Cells
3.3. Bortezomib Treatment Induces Hypermethylation at Specific Subset of CpG Sites
3.4. BTZ-Induced Methylation Changes Affect Genes Involved in Neurogenesis and Neurotransmission
3.5. Specific Transcription Factor Binding Sites Are Affected by BTZ-Induced Methylation Changes
3.6. CpGs with BTZ-Induced Methylation Changes May Affect Chromatin Structure
3.7. BTZ-Induced Methylation Changes Identified in dLUHMES Cells Are Not Affected by BTZ Treatment in the SH-SY5Y Cell Line
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Łuczkowska, K.; Taryma-Leśniak, O.; Bińkowski, J.; Sokołowska, K.E.; Strapagiel, D.; Jarczak, J.; Paczkowska, E.; Machaliński, B.; Wojdacz, T.K. Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells. Cancers 2022, 14, 3402. https://doi.org/10.3390/cancers14143402
Łuczkowska K, Taryma-Leśniak O, Bińkowski J, Sokołowska KE, Strapagiel D, Jarczak J, Paczkowska E, Machaliński B, Wojdacz TK. Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells. Cancers. 2022; 14(14):3402. https://doi.org/10.3390/cancers14143402
Chicago/Turabian StyleŁuczkowska, Karolina, Olga Taryma-Leśniak, Jan Bińkowski, Katarzyna E. Sokołowska, Dominik Strapagiel, Justyna Jarczak, Edyta Paczkowska, Bogusław Machaliński, and Tomasz K. Wojdacz. 2022. "Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells" Cancers 14, no. 14: 3402. https://doi.org/10.3390/cancers14143402