DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors
Abstract
:1. Introduction
2. Results
2.1. DNA Methylation Changes in miRNA Genes in Gonadotroph PitNETs
2.2. The Relationship between Impaired Methylation and Expression of miRNA Genes
2.3. Validating the Role of Selected Aberrantly Methylated miRNAs in a Large Patient Cohort
2.4. Predicting the mRNA Targets of Epigenetically Deregulated miRNAs
3. Discussion
4. Materials and Methods
4.1. Patients and Samples
4.2. Profiling Genome-Wide DNA Methylation with Microarray Technology
4.3. Assessment of miRNA Expression with Next Generation Sequencing (NGS)
4.4. Evaluation of DNA Methylation Pattern at Selected Genomic Regions
4.5. Determining miRNA Expression Level with qRT-PCR
4.6. miRNA Target-Prediction
4.7. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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HM450K CpG Site | CpG Location | miRNA | Discovery Group Spearman R; adj. p-Value | Validation Group Spearman R; p-Value |
---|---|---|---|---|
cg23121785 | TSS1500 | hsa-miR-184 | −0.577; adj. p = 0.0244 | −0.524; p < 0.0001 |
cg01310120 | TSS200 | hsa-miR-145-5p | −0.608; adj. p = 0.0163 | −0.312; p = 0.0061 |
cg23917868 | TSS200 | hsa-miR-145-5p | −0.672; adj. p = 0.0122 | −0.448; p < 0.0001 |
cg02515217 | TSS200 | hsa-miR-21-5p | −0,796; adj. p = 0.0011 | −0.336; p = 0.0030 |
Putative Onco-miRNAs Based on Identification of Target mRNAs in NCG 6.0 | |||||
---|---|---|---|---|---|
miRNA | DNA Methylation/Expression Results | Target Gene Prediction | |||
Methylation status in tumor | DNA methylation/expression relationship | Putative target mRNA | Correlation (Spearman R, non-adjusted p-value) | Confidence of target prediction with MirDIP | |
hsa-miR-134-5p | Hypomethylated | Positive | SCN9A | −0.531, 0.0080 | Very high |
hsa-miR-145-5p | Hypermethylated | Negative | MAP2K4 | −0.539, 0.0071 | Very high |
CDH2 | −0.515, 0.0100 | Very high | |||
hsa-miR-150-5p | Hypermethylated | Negative | CACNA2D1 | −0.514, 0.0102 | Very high |
hsa-miR-21-5p | Hypermethylated | Negative | RNF111 | −0.558, 0.0053 | Very high |
hsa-miR-23b-3p | Hypermethylated | Negative | CCDC6 | −0.505, 0.0116 | Very high |
Putative onco-miRNAs based on literature-based interpretation of role of target mRNA | |||||
miRNA | DNA Methylation/Expression Results | Target Gene Prediction | |||
Methylation status in tumor | DNA methylation/expression relationship | Putative target mRNA | Correlation (Spearman R, non-adjusted p-value) | Confidence of target prediction with MirDIP | |
hsa-miR-23b-3p | Hypermethylated | Negative | NACC1 | −0.510, 0.0107 | Very high |
PIK3R3 | −0.504, 0.0117 | Very high | |||
hsa-miR-134-5p | Hypomethylated | Positive | INA | −0.5103, 0.0107 | Very high |
Characteristic | Genome-Wide DNA Methylation/Whole Transcriptome Profiling | DNA Pyrosequencing/qRT-PCR |
---|---|---|
PitNET patients (number of patients) | 15 | 80 |
Age (years) | ||
Range | 36–73 | 34–80 |
Median | 57 | 61 |
Gender (number of patients) | ||
Male | 10 | 46 |
Female | 5 | 34 |
Histopathology (number of patients) | ||
Gonadotroph PA | 15 | 74 |
Null-cell/gonadotroph PA * | 0 | 6 |
Clinical classification (number of patients) | ||
Invasive NFPA | 5 | 49 |
Non-invasive NFPA | 10 | 25 |
Unknown | - | 6 |
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Boresowicz, J.; Kober, P.; Rusetska, N.; Maksymowicz, M.; Paziewska, A.; Dąbrowska, M.; Zeber-Lubecka, N.; Kunicki, J.; Bonicki, W.; Ostrowski, J.; et al. DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors. Life 2020, 10, 59. https://doi.org/10.3390/life10050059
Boresowicz J, Kober P, Rusetska N, Maksymowicz M, Paziewska A, Dąbrowska M, Zeber-Lubecka N, Kunicki J, Bonicki W, Ostrowski J, et al. DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors. Life. 2020; 10(5):59. https://doi.org/10.3390/life10050059
Chicago/Turabian StyleBoresowicz, Joanna, Paulina Kober, Natalia Rusetska, Maria Maksymowicz, Agnieszka Paziewska, Michalina Dąbrowska, Natalia Zeber-Lubecka, Jacek Kunicki, Wiesław Bonicki, Jerzy Ostrowski, and et al. 2020. "DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors" Life 10, no. 5: 59. https://doi.org/10.3390/life10050059