Mohammed Ismail Wazim, Fernandez Jenna A, Binder Moritz, Lasho Terra L, Kim Minsuk, Geyer Susan M, Mazzone Amelia, Finke Christy M, Mangaonkar Abhishek A, Lee Jeong-Heon, Wang Liguo, Kim Kwan Hyun, Simon Vernadette A, Rakhshan Rohakthar Fariborz, Munankarmy Amik, Byeon Seul Kee, Schwager Susan M, Harrington Jonathan J, Snyder Melissa R, Robertson Keith D, Pandey Akhilesh, Wieben Eric D, Chia Nicholas, Gaspar-Maia Alexandre, Patnaik Mrinal M
Department of Laboratory Medicine and Pathology, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN.
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
Blood Adv. 2025 Jan 28;9(2):402-416. doi: 10.1182/bloodadvances.2024014467.
DNMT3A and TET2 are epigenetic regulator genes commonly mutated in age-related clonal hematopoiesis (CH). Despite having opposed epigenetic functions, these mutations are associated with increased all-cause mortality and a low risk for progression to hematologic neoplasms. Although individual impacts on the epigenome have been described using different model systems, the phenotypic complexity in humans remains to be elucidated. Here, we make use of a natural inflammatory response occurring during coronavirus disease 2019 (COVID-19), to understand the association of these mutations with inflammatory morbidity (acute respiratory distress syndrome [ARDS]) and mortality. We demonstrate the age-independent, negative impact of DNMT3A mutant (DNMT3Amt) CH on COVID-19-related ARDS and mortality. Using single-cell proteogenomics we show that DNMT3A mutations involve myeloid and lymphoid lineage cells. Using single-cell multiomics sequencing, we identify cell-specific gene expression changes associated with DNMT3A mutations, along with significant epigenomic deregulation affecting enhancer accessibility, resulting in overexpression of interleukin-32 (IL-32), a proinflammatory cytokine that can result in inflammasome activation in monocytes and macrophages. Finally, we show with single-cell resolution that the loss of function of DNMT3A is directly associated with increased chromatin accessibility in mutant cells. Hence, we demonstrate the negative prognostic impact of DNMT3Amt CH on COVID-19-related ARDS and mortality. DNMT3Amt CH in the context of COVID-19, was associated with inflammatory transcriptional priming, resulting in overexpression of IL32. This overexpression was secondary to increased chromatic accessibility, specific to DNMT3Amt CH cells. DNMT3Amt CH can thus serve as a potential biomarker for adverse outcomes in COVID-19.
DNMT3A和TET2是在与年龄相关的克隆性造血（CH）中常见突变的表观遗传调节基因。尽管它们具有相反的表观遗传功能，但这些突变与全因死亡率增加和血液系统肿瘤进展风险较低相关。虽然已经使用不同的模型系统描述了它们对表观基因组的个体影响，但人类中的表型复杂性仍有待阐明。在这里，我们利用2019年冠状病毒病（COVID-19）期间发生的自然炎症反应，来了解这些突变与炎症性发病（急性呼吸窘迫综合征[ARDS]）和死亡率之间的关联。我们证明了DNMT3A突变型（DNMT3Amt）CH对COVID-19相关ARDS和死亡率的年龄独立的负面影响。使用单细胞蛋白质基因组学，我们表明DNMT3A突变涉及髓系和淋巴系细胞。使用单细胞多组学测序，我们确定了与DNMT3A突变相关的细胞特异性基因表达变化，以及影响增强子可及性的显著表观基因组失调，导致促炎细胞因子白细胞介素-32（IL-32）的过表达，IL-32可导致单核细胞和巨噬细胞中的炎性小体激活。最后，我们以单细胞分辨率表明，DNMT3A功能丧失与突变细胞中染色质可及性增加直接相关。因此，我们证明了DNMT3Amt CH对COVID-19相关ARDS和死亡率的负面预后影响。COVID-19背景下的DNMT3Amt CH与炎症转录启动相关，导致IL32过表达。这种过表达继发于DNMT3Amt CH细胞特有的染色质可及性增加。因此，DNMT3Amt CH可作为COVID-19不良结局的潜在生物标志物。
