| Literature DB >> 34393975 |
Hua Tao1,2, Zengqiang Chen1, Jianhao Wu1, Jun Chen1, Yusen Chen2, Jiawu Fu1, Chaowen Sun1, Haihong Zhou1, Wangtao Zhong1, Xu Zhou1,2, Keshen Li2,3.
Abstract
Epilepsy is characterized by highly abnormal synchronous discharge of brain neurons, and ion channels are fundamental in the generation and modulation of neural excitability. Considering that abnormal methylation can either activate or repress genes, this study was designed to explore the DNA methylation signature of pathogenic genes encoding ion channels in temporal lobe epilepsy (TLE). In total, 38 TLE patients and 38 healthy controls were enrolled in the study, and genomic DNA and total protein of the lymphocytes were extracted from peripheral blood samples to assess methylation and protein levels. The DNA methylation levels of all 12 genes examined were significantly lower in the TLE group than in the control group. After false-positive correction, 83.3% (10/12) of these genes, namely, gamma-aminobutyric acid type A receptor subunit beta1 (GABRB1), gamma-aminobutyric acid type A receptor subunit beta2 (GABRB2), gamma-aminobutyric acid type A receptor subunit beta1 (GABRB3), glutamate ionotropic receptor NMDA type subunit 1 (GRIN1), glutamate ionotropic receptor NMDA type subunit 2A (GRIN2A), glutamate ionotropic receptor NMDA type subunit 2B (GRIN2B), hyperpolarization activated cyclic nucleotide gated potassium channel 1 (HCN1), potassium voltage-gated channel subfamily A member 2 (KCNA2), potassium voltage-gated channel subfamily B member 1 (KCNB1), and potassium sodium-activated channel subfamily T member 1 (KCNT1), were still differentially expressed. Among these ion channels, HCN1 and KCNA2 were selected to evaluate the effects of DNA methylation, and the levels of these proteins were inversely upregulated in the TLE group compared to the control group. As the genes identified as having differential methylation levels are involved in both excitatory and inhibitory ion channels, this study observed by binary logistic regression that hypermethylated GARAB1 was an independent risk factor for TLE, indicating that the overwhelming effect of ion channels on TLE is probably inhibitory from the perspective of DNA methylation. All these findings support the involvement of DNA methylation in TLE pathologies, but the mechanisms need to be further investigated.Entities:
Keywords: DNA methylation; epigenetic; genetic susceptibility; ion channels; temporal lobe epilepsy
Year: 2021 PMID: 34393975 PMCID: PMC8358672 DOI: 10.3389/fneur.2021.692412
Source DB: PubMed Journal: Front Neurol ISSN: 1664-2295 Impact factor: 4.003
General characteristics of enrolled individuals.
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| Sex (male/female, | 18/20 | 19/19 | 0.818 |
| Age (mean ± SD, years old) | 32.1 ± 14.4 | 33.4 ± 6.4 | 0.602 |
| Young (<26 years old) | 20.2 ± 3.3 | - | - |
| Old (≥26 years old) | 44.0 ± 10.8 | - | - |
| Age at onset (mean ± SD, years old) | 23.3 ± 16.2 | - | - |
| Early-onset (<18 years old) | 12.0 ± 5.2 | - | - |
| Late-onset (≥18 years old) | 34.6 ± 15.5 | - | - |
| Disease duration (mean ± SD, years) | 8.8 ± 9.8 | - | - |
| Short duration (<5 years) | 1.3 ± 1.5 | - | - |
| Long duration (≥5 years) | 16.3 ± 8.8 | - | - |
| Drug response (n) | 38 | - | - |
| Sensitive patients | 24 | - | - |
| Resistant patients | 14 | - | - |
DNA methylation status of 12 ion-channel genes between TLE cases and controls.
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| 1.62 ± 0.52 | 2.39 ± 0.81 | 0.68 | 0.0000 | 0.0001 |
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| 4.80 ± 0.96 | 6.28 ± 1.26 | 0.77 | 0.0000 | 0.0001 |
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| 18.23 ± 2.14 | 20.29 ± 2.74 | 0.90 | 0.0005 | 0.0057 |
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| 23.10 ± 2.96 | 25.62 ± 3.25 | 0.90 | 0.0007 | 0.0087 |
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| 2.96 ± 0.43 | 3.67 ± 0.76 | 0.81 | 0.0000 | 0.0000 |
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| 4.07 ± 0.96 | 5.60 ± 1.74 | 0.73 | 0.0000 | 0.0001 |
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| 4.43 ± 1.05 | 5.61 ± 1.42 | 0.79 | 0.0001 | 0.0011 |
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| 1.02 ± 0.09 | 1.18 ± 0.13 | 0.87 | 0.0000 | 0.0000 |
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| 21.50 ± 0.26 | 21.78 ± 0.35 | 0.99 | 0.0002 | 0.0025 |
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| 1.12 ± 0.12 | 1.18 ± 0.10 | 0.96 | 0.0456 | 0.5473 |
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| 17.10 ± 1.60 | 19.03 ± 2.42 | 0.90 | 0.0001 | 0.0012 |
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| 0.82 ± 0.06 | 0.82 ± 0.07 | 1.00 | 0.8262 | 9.9148 |
Methylation details of 12 ion-channel genes between TLE cases and controls.
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| 1 | 16 | 10 | 21 | 3 |
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| 2 | 26 | 24 | 17 | 6 |
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| 3 | 86 | 66 | 133 | 7 |
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| 1 | 16 | 12 | 32 | 4 |
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| 3 | 69 | 37 | 34 | 4 |
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| 4 | 59 | 26 | 66 | 4 |
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| 2 | 34 | 22 | 44 | 4 |
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| 2 | 28 | 17 | 24 | 4 |
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| 3 | 61 | 19 | 17 | 0 |
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| 1 | 59 | 6 | 61 | 7 |
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| 1 | 21 | 16 | 6 | 4 |
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| 1 | 23 | 0 | 20 | 0 |
Independent risk factors for DNA methylation-related ion channels evaluated by binary logistic regression.
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| Step 1 | Sex | 0.566 | 0.709 | 0.637 | 1 | 0.425 | 1.761 | 0.439 | 7.064 |
| Age | 0.049 | 0.035 | 1.979 | 1 | 0.159 | 1.051 | 0.981 | 1.125 | |
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| −140.522 | 65.451 | 4.61 | 1 | 0.032 | 9.37E−62 | 1.82E−117 | 4.83E−6 | |
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| −58.759 | 96.787 | 0.369 | 1 | 0.544 | 3.03E−26 | 1.25E−108 | 7.35E+56 | |
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| 22.54 | 28.75 | 0.615 | 1 | 0.433 | 6.15E+09 | 2.07E−15 | 1.82E+34 | |
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| −2.823 | 15.721 | 0.032 | 1 | 0.858 | 0.059 | 2.47E−15 | 1.43E+12 | |
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| −74.74 | 124.206 | 0.362 | 1 | 0.547 | 3.47E−33 | 6.55E−139 | 1.84E+73 | |
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| −81.974 | 57.44 | 2.037 | 1 | 0.154 | 2.51E−36 | 3.21E−85 | 1.96E+13 | |
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| 106.495 | 67.541 | 2.486 | 1 | 0.115 | 1.78E+46 | 5.74E−12 | 5.51E+103 | |
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| −1097.276 | 609.439 | 3.242 | 1 | 0.072 | 0.000 | 0.000 | 1.64E+42 | |
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| −103.195 | 169.724 | 0.37 | 1 | 0.543 | 1.52E−45 | 5.17E−190 | 4.49E+99 | |
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| −2.542 | 19.018 | 0.018 | 1 | 0.894 | 0.079 | 5.10E−18 | 1.22E+15 | |
| Constant | 35.547 | 36.864 | 0.93 | 1 | 0.335 | 2.74E+15 | |||
Variables in step 1: Sex, Age, GABRB1, GABRB2, GABRB3, GRIN1, GRIN2A, GRIN2B, HCN1, KCNA2, KCNB1, KCNT1.
DNA methylation of 12 ion-channel genes between young and old patients.
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| 1.41 ± 0.39 | 1.83 ± 0.54 | 0.80 | 0.0125 |
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| 4.25 ± 0.46 | 5.35 ± 0.99 | 0.80 | 0.0001 |
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| 17.35 ± 1.67 | 19.11 ± 2.14 | 0.91 | 0.0093 |
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| 22.12 ± 2.86 | 24.09 ± 2.64 | 0.93 | 0.0388 |
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| 2.78 ± 0.27 | 3.14 ± 0.47 | 0.89 | 0.0083 |
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| 3.87 ± 0.80 | 4.26 ± 1.04 | 0.89 | 0.2083 |
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| 4.01 ± 0.67 | 4.84 ± 1.17 | 0.84 | 0.0125 |
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| 0.99 ± 0.07 | 1.05 ± 0.10 | 0.96 | 0.0592 |
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| 21.40 ± 0.22 | 21.60 ± 0.26 | 0.99 | 0.0151 |
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| 1.13 ± 0.13 | 1.11 ± 0.11 | 1.00 | 0.5715 |
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| 16.92 ± 1.44 | 17.28 ± 1.69 | 0.98 | 0.5008 |
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| 0.81 ± 0.06 | 0.82 ± 0.05 | 0.96 | 0.5090 |
DNA methylation of 12 ion-channel genes between short and long duration of disease.
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| 1.41 ± 0.37 | 1.78 ± 0.56 | 0.80 | 0.0351 |
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| 4.52 ± 0.85 | 4.89 ± 0.97 | 0.93 | 0.2026 |
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| 17.62 ± 2.21 | 18.50 ± 1.89 | 0.95 | 0.2108 |
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| 22.40 ± 3.26 | 23.40 ± 2.48 | 0.96 | 0.2986 |
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| 2.91 ± 0.52 | 2.97 ± 0.32 | 0.98 | 0.7003 |
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| 4.20 ± 0.93 | 3.95 ± 0.95 | 1.06 | 0.4447 |
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| 4.09 ± 0.95 | 4.63 ± 1.03 | 0.88 | 0.1219 |
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| 1.00 ± 0.08 | 1.025 ± 0.09 | 0.99 | 0.6087 |
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| 21.46 ± 0.26 | 21.55 ± 0.25 | 1.00 | 0.2897 |
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| 1.11 ± 0.10 | 1.12 ± 0.15 | 1.02 | 0.6275 |
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| 17.38 ± 1.09 | 16.79 ± 1.85 | 1.04 | 0.2840 |
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| 0.81 ± 0.06 | 0.82 ± 0.06 | 1.00 | 0.9887 |
Figure 1Protein levels of selected ion channel genes in peripheral blood using ELISA. The protein levels of HCN1 and KCNA2 in the TLE group reached a significant level, with a 1.3-fold change and 1.5-fold change in comparison with the control group, respectively (A). Within the TLE group, the levels of HCN1 protein were significantly increased in the young patients and in the early-onset patients (C,D); expression of KCNA2 was also significantly upregulated in young patients compared with old patients (D), but no differences in HCN1 and KCNA2 were observed in accordance with stratified analysis of sex (B), disease duration (E), or drug response (F). *p < 0.05; ***p < 0.001.