Potential epigenetic biomarkers of obesity-related insulin resistance in human whole-blood

Obesity can increase the risk of complex metabolic diseases, including insulin resistance. Moreover, obesity can be caused by environmental and genetic factors. However, the epigenetic mechanisms of obesity are not well defined. Therefore, the identification of novel epigenetic biomarkers of obesity allows for a more complete understanding of the disease and its underlying insulin resistance. The aim of our study was to identify DNA methylation changes in whole-blood that were strongly associated with obesity and insulin resistance. Whole-blood was obtained from lean (n = 10; BMI = 23.6 ± 0.7 kg/m²) and obese (n = 10; BMI = 34.4 ± 1.3 kg/m²) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing on genomic DNA isolated from the blood. We identified 49 differentially methylated cytosines (DMCs; q &lt; 0.05) that were altered in obese compared with lean participants. We identified 2 sites (Chr.21:46,957,981 and Chr.21:46,957,915) in the 5’ untranslated region of solute carrier family 19 member 1 (<i>SLC19A1</i>) with decreased methylation in obese participants (lean 0.73 ± 0.11 vs. obese 0.09 ± 0.05; lean 0.68 ± 0.10 vs. obese 0.09 ± 0.05, respectively). These 2 DMCs identified by obesity were also significantly predicted by insulin sensitivity (r = 0.68, <i>P = 0.003</i>; r = 0.66; <i>P = 0.004</i>). In addition, we performed a differentially methylated region (DMR) analysis and demonstrated a decrease in methylation of Chr.21:46,957,915–46,958,001 in <i>SLC19A1</i> of −34.9% (70.4% lean vs. 35.5% obese). The decrease in whole-blood <i>SLC19A1</i> methylation in our obese participants was similar to the change observed in skeletal muscle (Chr.21:46,957,981, lean 0.70 ± 0.09 vs. obese 0.31 ± 0.11 and Chr.21:46,957,915, lean 0.72 ± 0.11 vs. obese 0.31 ± 0.13). Pyrosequencing analysis further demonstrated a decrease in methylation at Chr.21:46,957,915 in both whole-blood (lean 0.71 ± 0.10 vs. obese 0.18 ± 0.06) and skeletal muscle (lean 0.71 ± 0.10 vs. obese 0.30 ± 0.11). Our findings demonstrate a new potential epigenetic biomarker, <i>SLC19A1</i>, for obesity and its underlying insulin resistance.

肥胖可增加包括胰岛素抵抗（insulin resistance）在内的复杂代谢疾病的发病风险，且肥胖的发生可由环境与遗传因素共同介导。然而，目前肥胖的表观遗传（epigenetic）调控机制尚未得到充分阐明。因此，鉴定肥胖的新型表观遗传生物标志物，有助于更全面地理解该疾病及其伴随的胰岛素抵抗。
本研究的核心目的为鉴定与肥胖及胰岛素抵抗显著相关的全血DNA甲基化（DNA methylation）变化。我们从体重正常（n=10；BMI=23.6±0.7 kg/m²）与肥胖（n=10；BMI=34.4±1.3 kg/m²）受试者中采集全血样本，并结合正常血糖高胰岛素钳夹试验评估受试者的胰岛素敏感性。
我们对从血液中分离得到的基因组DNA开展了简化代表性亚硫酸氢盐测序（reduced representation bisulfite sequencing），最终鉴定出49个在肥胖受试者与体重正常受试者间存在差异的甲基化胞嘧啶（differentially methylated cytosines, DMCs；q<0.05）。其中，在溶质载体家族19成员1（solute carrier family 19 member 1, SLC19A1）的5'非翻译区（5’ untranslated region）中，我们发现2个位点（Chr.21:46,957,981与Chr.21:46,957,915）在肥胖受试者中呈现甲基化水平降低的现象，体重正常组与肥胖组的甲基化水平分别为0.73±0.11 vs 0.09±0.05、0.68±0.10 vs 0.09±0.05。
这2个因肥胖筛选得到的DMCs同样可显著预测胰岛素敏感性（相关系数r=0.68，P=0.003；r=0.66，P=0.004）。此外，我们开展了差异甲基化区域（differentially methylated region, DMR）分析，结果显示SLC19A1中Chr.21:46,957,915–46,958,001区域的甲基化水平降低了34.9%（体重正常组为70.4%，肥胖组为35.5%）。
本研究中肥胖受试者全血SLC19A1的甲基化水平降低趋势，与骨骼肌中观察到的变化一致：Chr.21:46,957,981位点的甲基化水平，体重正常组为0.70±0.09，肥胖组为0.31±0.11；Chr.21:46,957,915位点的甲基化水平，体重正常组为0.72±0.11，肥胖组为0.31±0.13。
焦磷酸测序（pyrosequencing）分析进一步证实，全血与骨骼肌中Chr.21:46,957,915位点的甲基化水平均显著降低：全血样本中，体重正常组为0.71±0.10，肥胖组为0.18±0.06；骨骼肌样本中，体重正常组为0.71±0.10，肥胖组为0.30±0.11。
本研究结果表明，SLC19A1可作为肥胖及其伴随胰岛素抵抗的新型潜在表观遗传生物标志物。