Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No.1 Shuaifuyuan, Beijing, 100730, China.
Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Changping District, Beijing, 102206, China.
Clin Epigenetics. 2024 Mar 1;16(1):37. doi: 10.1186/s13148-024-01645-7.
The recently identified methylation patterns specific to cell type allows the tracing of cell death dynamics at the cellular level in health and diseases. This study used COVID-19 as a disease model to investigate the efficacy of cell-specific cell-free DNA (cfDNA) methylation markers in reflecting or predicting disease severity or outcome.
Whole genome methylation sequencing of cfDNA was performed for 20 healthy individuals, 20 cases with non-hospitalized COVID-19 and 12 cases with severe COVID-19 admitted to intensive care unit (ICU). Differentially methylated regions (DMRs) and gene ontology pathway enrichment analyses were performed to explore the locus-specific methylation difference between cohorts. The proportion of cfDNA derived from lung and immune cells to a given sample (i.e. tissue fraction) at cell-type resolution was estimated using a novel algorithm, which reflects lung injuries and immune response in COVID-19 patients and was further used to evaluate clinical severity and patient outcome.
COVID‑19 patients had globally reduced cfDNA methylation level compared with healthy controls. Compared with non-hospitalized COVID-19 patients, the cfDNA methylation pattern was significantly altered in severe patients with the identification of 11,156 DMRs, which were mainly enriched in pathways related to immune response. Markedly elevated levels of cfDNA derived from lung and more specifically alveolar epithelial cells, bronchial epithelial cells, and lung endothelial cells were observed in COVID-19 patients compared with healthy controls. Compared with non-hospitalized patients or healthy controls, severe COVID-19 had significantly higher cfDNA derived from B cells, T cells and granulocytes and lower cfDNA from natural killer cells. Moreover, cfDNA derived from alveolar epithelial cells had the optimal performance to differentiate COVID-19 with different severities, lung injury levels, SOFA scores and in-hospital deaths, with the area under the receiver operating characteristic curve of 0.958, 0.941, 0.919 and 0.955, respectively.
Severe COVID-19 has a distinct cfDNA methylation signature compared with non-hospitalized COVID-19 and healthy controls. Cell type-specific cfDNA methylation signature enables the tracing of COVID-19 related cell deaths in lung and immune cells at cell-type resolution, which is correlated with clinical severities and outcomes, and has extensive application prospects to evaluate tissue injuries in diseases with multi-organ dysfunction.
最近发现的细胞类型特异性甲基化模式允许在健康和疾病状态下在细胞水平上追踪细胞死亡动力学。本研究以 COVID-19 为疾病模型，研究细胞游离 DNA（cfDNA）甲基化标记物在反映或预测疾病严重程度或结局方面的功效。
对 20 名健康个体、20 名非住院 COVID-19 患者和 12 名入住重症监护病房（ICU）的严重 COVID-19 患者的 cfDNA 进行全基因组甲基化测序。通过差异甲基化区域（DMR）和基因本体通路富集分析，探讨队列之间局灶性甲基化差异。使用一种新算法估计 cfDNA 来源于特定样本（即组织分数）中肺细胞和免疫细胞的比例，该算法反映了 COVID-19 患者的肺损伤和免疫反应，并进一步用于评估临床严重程度和患者结局。
与健康对照组相比，COVID-19 患者的 cfDNA 甲基化水平普遍降低。与非住院 COVID-19 患者相比，严重 COVID-19 患者的 cfDNA 甲基化模式发生了显著改变，鉴定出 11156 个 DMR，主要富集在与免疫反应相关的通路中。与健康对照组相比，COVID-19 患者 cfDNA 来源于肺的水平显著升高，特别是肺泡上皮细胞、支气管上皮细胞和肺内皮细胞。与非住院患者或健康对照组相比，严重 COVID-19 患者 cfDNA 来源于 B 细胞、T 细胞和粒细胞的水平显著升高，而来源于自然杀伤细胞的 cfDNA 水平显著降低。此外，cfDNA 来源于肺泡上皮细胞对区分不同严重程度、肺损伤程度、SOFA 评分和住院死亡的 COVID-19 具有最佳性能，其受试者工作特征曲线下面积分别为 0.958、0.941、0.919 和 0.955。
与非住院 COVID-19 和健康对照组相比，严重 COVID-19 具有明显的 cfDNA 甲基化特征。细胞特异性 cfDNA 甲基化特征能够以细胞分辨率追踪 COVID-19 相关的肺和免疫细胞死亡，与临床严重程度和结局相关，并具有广泛的应用前景，可用于评估多器官功能障碍疾病中的组织损伤。
