A promising application of kidney-specific cell-free DNA methylation markers in real-time monitoring sepsis-induced acute kidney injury

Sepsis-induced acute kidney injury (SI-AKI) is a common clinical syndrome that is associated with high mortality and morbidity. Effective timely detection may improve the outcome of SI-AKI. Kidney-derived cell-free DNA (cfDNA) may provide new insight into understanding and identifying SI-AKI. Plasma cfDNA from 82 healthy individuals, 7 patients with sepsis non-acute kidney injury (SN-AKI), and 9 patients with SI-AKI was subjected to genomic methylation sequencing. We deconstructed the relative contribution of cfDNA from different cell types based on cell-specific methylation markers and focused on exploring the association between kidney-derived cfDNA and SI-AKI.Based on the deconvolution of the cfDNA methylome: SI-AKI patients displayed the elevated cfDNA concentrations with an increased contribution of kidney epithelial cells (kidney-Ep) DNA; kidney-Ep derived cfDNA achieved high accuracy in distinguishing SI-AKI from SN-AKI (AUC = 0.92, 95% CI 0.7801–1); the higher kidney-ep cfDNA concentrations tended to correlate with more advanced stages of SI-AKI; strikingly, SN-AKI patients with potential kidney damage unmet by SI-AKI criteria showed higher levels of kidney-Ep derived cfDNA than healthy individuals. The autonomous screening of kidney-Ep (<i>n</i> = 24) and kidney endothelial (kidney-Endo, <i>n</i> = 12) specific methylation markers indicated the unique identity of kidney-Ep/kidney-Endo compared with other cell types, and its targeted assessment reproduced the main findings of the deconvolution of the cfDNA methylome. Our study first demonstrates that kidney-Ep- and kidney-Endo-specific methylation markers can serve as a novel marker for SI-AKI emergence, supporting further exploration of the utility of kidney-specific cfDNA methylation markers in the study of SI-AKI.

脓毒症诱导急性肾损伤（Sepsis-induced acute kidney injury, SI-AKI）是一类临床常见综合征，具有较高的病死率与发病率。及时实施有效的检测或可改善SI-AKI患者的预后。肾脏来源游离脱氧核糖核酸（cell-free DNA, cfDNA）或可为理解与识别SI-AKI提供全新的研究视角。本研究对82名健康个体、7名脓毒症非急性肾损伤（sepsis non-acute kidney injury, SN-AKI）患者以及9名SI-AKI患者的血浆cfDNA开展了全基因组甲基化测序。基于细胞特异性甲基化标记物，本研究解析了不同细胞类型来源cfDNA的相对贡献占比，并重点探讨了肾脏来源cfDNA与SI-AKI之间的关联。基于cfDNA甲基化组的解卷积分析结果显示：SI-AKI患者的cfDNA浓度升高，且肾脏上皮细胞（kidney epithelial cells, kidney-Ep）来源DNA的占比显著提升；肾脏上皮细胞来源cfDNA可精准区分SI-AKI与SN-AKI（曲线下面积（Area Under Curve, AUC）=0.92，95%置信区间（Confidence Interval, CI）0.7801–1）；肾脏上皮细胞来源cfDNA浓度越高，往往对应SI-AKI的病情分期越晚；值得注意的是，部分符合潜在肾损伤但未达到SI-AKI诊断标准的SN-AKI患者，其肾脏上皮细胞来源cfDNA水平高于健康个体。对肾脏上皮细胞（样本量n=24）与肾脏内皮细胞（kidney endothelial, kidney-Endo，样本量n=12）的特异性甲基化标记物进行自主筛选后发现，相较于其他细胞类型，肾脏上皮细胞/肾脏内皮细胞具有独特的分子特征，且针对该类标记物的靶向评估重现了cfDNA甲基化组解卷积分析的核心发现。本研究首次证实，肾脏上皮细胞与肾脏内皮细胞特异性甲基化标记物可作为SI-AKI发生的新型生物标志物，为进一步探索肾脏特异性cfDNA甲基化标记物在SI-AKI研究中的应用价值提供了支撑。