Genetic and Epigenetic Aberrations of SOX7 in Newly Diagnosed and Relapsed Multiple Myeloma as Well as Related Neoplasms
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Information
2.2. Chemicals and Reagents
2.3. FACS Sorting of Bone Marrow Tumor Cells
2.4. Isolation of DNA and RNA from MM Bone Marrow Tumor Cells
2.5. Quality Control of the MM Bone Marrow Tumor Cell DNA and RNA
2.6. Tonsil Samples from Control Cases
2.7. Tonsil PC Separations Through FACS
2.8. SOX7 Copy Number Analyses of Publicly Available SNP Array Data of Diagnostic MM Cases
2.9. SOX7 Deletion Analyses in Diagnostic and Relapsed MM Cases with qPCR
2.10. Promoter Methylation Analyses of SOX7 Using Publicly Available Methylation Array Data of MM and PCL
2.11. Integrated Analyses of Copy Number, Promoter Methylation, and Transcript Expression of the Candidate Tumor Suppressors Located in del8p23.1 in Diagnostic and Relapsed MM Cases
2.12. Evaluation of SOX7 mRNA Expression Levels Through Reanalyses of the Publicly Available GEP Data of Plasma Cell Neoplasms and Normal Plasma Cells
2.13. Evaluation of SOX7 mRNA Levels in Diagnostic and Relapsed MM Tumor Samples with qRT-PCR
2.14. Mutation Data of MM Samples
2.15. Evaluation of SOX7 mRNA Expression Levels in MM Cell Lines
2.16. Generation of Graphs and Statistical Analyses
3. Results
3.1. SOX7 Deletions Are Frequent in Diagnostic and Relapsed MM Samples
3.2. SOX7 Promoter Is Hypermethylated in Plasma Cell Malignancies
3.3. Deletion and Promoter Methylation of SOX7 Tend to Occur in Different MM Cases
3.4. The Influence of Deletion and Methylation on Expression of Candidate Tumor Suppressors in 8p23.1
3.5. Mutations of SOX7 Are Infrequent in MM Tumor Samples
3.6. SOX7 Is Transcriptionally Silent in MM Cell Lines
3.7. SOX7 Was Underexpressed in MM and High-Risk SMM Compared to Normal PCs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
MM | Multiple myeloma |
SMM | Smoldering multiple myeloma |
PCL | Plasma cell leukemia |
CRC | Colorectal cancer |
QC | Quality check |
ACK | Ammonium–chloride–potassium |
MACS | Magnetic-activated cell sorting |
GEP | Gene expression profiling |
OSA | Obstructive sleep apnea |
HDAC | Histone deacetylase |
NGS | Next-generation sequencing |
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Küçük, C.; Akman, B.; Hu, X.; Hatipoğlu, T.; Şeyhanlı, A.; Ceylan, A.; Yılmaz, B.; Öztürk, O.C.; Erdağ, T.K.; Özsan, G.H. Genetic and Epigenetic Aberrations of SOX7 in Newly Diagnosed and Relapsed Multiple Myeloma as Well as Related Neoplasms. Curr. Issues Mol. Biol. 2025, 47, 244. https://doi.org/10.3390/cimb47040244
Küçük C, Akman B, Hu X, Hatipoğlu T, Şeyhanlı A, Ceylan A, Yılmaz B, Öztürk OC, Erdağ TK, Özsan GH. Genetic and Epigenetic Aberrations of SOX7 in Newly Diagnosed and Relapsed Multiple Myeloma as Well as Related Neoplasms. Current Issues in Molecular Biology. 2025; 47(4):244. https://doi.org/10.3390/cimb47040244
Chicago/Turabian StyleKüçük, Can, Burcu Akman, Xiaozhou Hu, Tevfik Hatipoğlu, Ahmet Şeyhanlı, Arda Ceylan, Bircan Yılmaz, Osman Can Öztürk, Taner Kemal Erdağ, and Güner Hayri Özsan. 2025. "Genetic and Epigenetic Aberrations of SOX7 in Newly Diagnosed and Relapsed Multiple Myeloma as Well as Related Neoplasms" Current Issues in Molecular Biology 47, no. 4: 244. https://doi.org/10.3390/cimb47040244
APA StyleKüçük, C., Akman, B., Hu, X., Hatipoğlu, T., Şeyhanlı, A., Ceylan, A., Yılmaz, B., Öztürk, O. C., Erdağ, T. K., & Özsan, G. H. (2025). Genetic and Epigenetic Aberrations of SOX7 in Newly Diagnosed and Relapsed Multiple Myeloma as Well as Related Neoplasms. Current Issues in Molecular Biology, 47(4), 244. https://doi.org/10.3390/cimb47040244