Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion [scATAC-Seq]

SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19. Overall design: Identify transcriptomic and epigenetic profiles of sub-populations of CD14+ monocytes that distinguished IgG- subjects with mild from moderate symptoms.

新型冠状病毒（SARS-CoV-2）感染会在人类宿主中引发强烈且个体差异显著的免疫应答。此前已有研究在重症或康复期新型冠状病毒肺炎（COVID-19）患者中观察到染色质重塑（Chromatin remodeling）现象，但在疾病早期、抗刺突蛋白IgG血清阳转（anti-spike protein IgG seroconversion）之前的染色质重塑特征尚未明确。
本研究对不同临床病程阶段的轻中度症状门诊患者的外周血单个核细胞（PBMCs）开展了转座酶可及性测序测定（ATAC-seq）与RNA测序（RNA-seq）。在IgG血清阳转前的疾病早期阶段，与轻中度症状相关的染色质可及性改变已十分显著，涉及白细胞介素信号通路、细胞分化调控及细胞形态相关基因的可及性变化，且存在与疾病严重程度相关的差异。
此外，单细胞分析揭示了不同时间点下各外周血单个核细胞类型的染色质可及性图谱与转录因子基序可及性的动态演变。其中染色质重塑程度最显著的是CD14+单核细胞，在血清阳转前即可观察到具有独特染色质可及性特征的亚群。
轻度症状患者以经典抗病毒通路的上调为特征，包括调控干扰素调节因子1（IRF1）与干扰素调节因子7（IRF7）的通路；而中度症状患者的这类经典抗病毒信号则有所减弱，提示机体免疫应答存在失调且效率降低。
综上，本研究为早期轻中度新型冠状病毒感染的表观基因组提供了全新见解，并提示早期疾病中染色质重塑的检测有望成为新型冠状病毒肺炎诊断的一类新型技术手段。
总体设计：鉴定可区分IgG阴性轻、中度症状患者的CD14+单核细胞亚群的转录组与表观遗传特征。