Longitudinal IFN signature response and cytokine profiling in patients with severe COVID infections

在与NIAID COVID联盟的合作下，我们分析了从84名严重COVID住院的成人患者中收集的纵向采集的全血样本以进行RNA分离。 我们还评估了来自布雷西亚(Brescia n=567)、蒙扎(Monza 77)和帕维亚(Pavia：43)严重冠状病毒感染住院的成年患者的血清样本中的血清IL-18、IL-18BP和CXCL-9，以及从先天和获得性免疫细胞和/或周围组织释放的Spike-2蛋白水平和其他炎症标志物的亚组。我们的数据显示，在住院患者中，I型干扰素信号总体上减少，NFKB和II型干扰素(干扰素-γ)调节基因的免疫激活程度不同，但在轻度疾病患者和健康对照组中没有(Abers等人)。JCI Insight 2021)。 分析28个I型干扰素调节基因的转录得分，发现部分患者的转录得分高于健康对照组，但新冠肺炎患者的I型干扰素得分显著低于单基因I型干扰素病。我们还发现，循环白细胞中IFNa2的标准化转录水平与血液中的干扰素-2a蛋白水平没有相关性。此外，在新冠肺炎患者中，正常化的IFNa2转录本仅与28个基因的I型干扰素得分弱相关，这与单基因干扰素病患者的显著相关性以及其他人(10，16，19)报道的新冠肺炎患者循环中血浆细胞样树突状细胞(PDC)数量减少和循环pDC产生I型干扰素的障碍相反，提示COVID患者非造血来源的干扰素。 对患者第一批样本的多变量分析显示，12种生物标志物与全身和单核细胞激活(sTNFRSF1A、IL-6、CCL2、铁蛋白、IL-15)、损伤(MMP-9、可溶性ST2 Sst2)、中性粒细胞激活(NGAL、S100A9)、内皮激活(SVEGFR1)和T细胞激活(IL-2)相关，与疾病严重程度和死亡率相关。其中，在住院期间，死亡患者的Sst2、sTNFRSF1A、IL-10和IL-15水平始终高于康复患者。(Abers等人)JCI Insight 2020)。 低水平的干扰素-α反应是导致COVID19严重疾病表现的原因之一。在另一项联合研究中，患有2019年危及生命的冠状病毒疾病的干扰素水平特别低并因此受损的患者的一部分患者在危重疾病开始时，10.2%的队列患者中有中和免疫球蛋白G(IgG)自身抗体(自动抗体)对抗干扰素-(干扰素-)、13种干扰素-或两者兼而有之。自体抗体在体外中和相应的I型IFN阻断SARS-CoV-2感染的能力。在600多名无症状或轻度感染SARS-CoV-2的患者中未发现这些自身抗体。(私生子等人)科学2020)。这项研究确定了抗I型干扰素抗体的存在是抑制干扰素反应的危险因素，并与其他宿主因素一起易患严重的COVD19。 一项多机构联合的纵向研究显示，急性新冠肺炎患者(n=110)和管理信息系统-C组(n=76)与儿科健康对照组(n=76)比较，急性新冠肺炎患者表现出强健的I型干扰素应答基因特征，而显著的II型干扰素依赖和核因子-B依赖特征，基质激活和循环尖峰蛋白水平增加，与入院时SARS-CoV-2聚合酶链式反应状态无关。研究进一步表明，TRBV11-2 T细胞克隆型在MIS-C中的瞬时扩张与炎症和T细胞激活的特征相关，并与HLAA*02、B*35和C*04等位基因的组合相关，表明MISC的发生具有遗传易感性。 切尔托小组与Chertow合作，评估了在COVID大流行早期进入ICU的插管式严重呼吸道感染患者的上呼吸道(URT)和下呼吸道(LRT)对SARS-CoV-2的先天免疫反应。我们同时评估了鼻咽、气管抽吸物和血液中I型干扰素(IFNa2和IFNB1)和II型干扰素(IFNG表达)的表达以及I型干扰素和核因子-B信号的诱导。我们比较了门诊轻度COVID19患者和重症新冠肺炎住院患者上呼吸道的天然免疫反应。我们进一步描述了上呼吸道和下呼吸道(LRT)以及血液中这些反应的每周动态变化，以确定间隔的差异。我们观察到，与疾病早期的重症患者相比，轻度患者的城市轨道交通中ISG和核因子-B的反应显著增加。轻度患者URT中IFNa2和IFNG表达增加，重度患者URT中IFNB1和STIN/IRF3/cGAS表达显著增加。重症患者的跨隔周分析显示，尽管IFNa2、IFNB1和IFNG在血液中的表达显著降低，但在疾病的第一周，这些患者的血液中的ISG反应显著高于URT和LRT。然而，在病情高峰期(第2周)，与URT和重症患者的血液相比，LRT组的核因子-B反应显著升高。我们的数据支持，严重的新冠肺炎与早期疾病期间URT中干扰素信号的受损以及疾病高峰期LRT中强烈的促炎反应有关(Ramos-Benitez MJ等人)。MedRxiv DOI：https://doi.org/10.1101/2022.11.08.22281846).

In collaboration with the NIAID COVID consortium we have analyzed longitudinally collected whole blood samples collected for RNA isolation from 84 adult patients hospitalized with severe COVID. We also assessed serum samples from a larger panel of adult patients hospitalized with severe COVID (from Brescia n=567, Monza 77 and Pavia: 43) for serum IL-18, IL-18BP and CXCL-9 and a subset for spike-2 protein levels and other inflammatory markers released from innate and adaptive immune cells and/or surrounding tissues. Our data showed overall reduced Type I IFN signaling and variably immune activation of NFKB and Type II IFN (IFN gamma) regulated genes in hospitalized patients but not in patients with milder disease and healthy controls (Abers et al. JCI Insight 2021). The transcriptional score derived from the analysis of 28 type I IFNregulated genes, was increased in a subset of patient over healthy controls but the type I IFN score of COVID-19 patients was significantly lower than that observed in monogenic type I IFNopathies. We also found that the normalized transcriptional levels of IFNA2 of circulating leukocytes did not correlate with the protein IFN-2a blood levels. Furthermore, normalized IFNA2 transcripts only weakly correlated with the 28-gene type I IFN score in COVID-19 patients which was in contrast to their significant correlation in patients with monogenic IFNopathies together with the decreased numbers of circulating plasmacytoid DCs (pDCs) and impaired production of type I IFN by circulating pDCs in COVID-19 patients reported by others (10, 16, 19) suggested non-hematopoietic sources of IFN alpha in COVID patients. A multivariable analysis of patients first samples revealed 12 biomarker-associated with systemic and monocyte activation (sTNFRSF1A, IL-6, CCL2, ferritin, IL-15), damage (MMP-9, soluble ST2 sST2), neutrophil activation (NGAL, S100A9) endothelial activation (sVEGFR1) and T cell activation (IL-2) correlated with disease severity and mortality. Among these, sST2, sTNFRSF1A, IL-10, and IL-15 were consistently higher throughout the hospitalization in patients who died versus those who recovered. (Abers et al. JCI Insight 2020). The inadequately low IFN alpha response contributes to the severe disease manifestations of COVID19. In another consortium study a subset of patients with particularly low and therefore impaired IFN who had life-threatening coronavirus disease 2019 had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon- (IFN-), 13 types of IFN- or against both in 10.2% of the cohort patients at the onset of critical disease. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in over 600 individuals with asymptomatic or mild SARS-CoV-2 infection. (Bastard et al. Science 2020). This study identified the presence of anti-type I IFN antibodies as risk factors that suppress the IFN response and with among other host factors predisposes to severe COVD19. A longitudinal multi-institutional consortium study conducted in pediatric patients with acute COVID-19 (n=110) and with MIS-C (n=76) and compared to pediatric healthy controls (pHCs; n=76) showed that acute COVID-19 patients mounted a robust type I interferon (IFN) response gene signature, whereas prominent type II IFN-dependent and NF-B-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission. The study further showed transient expansion of TRBV11-2 T cell clonotypes in MIS-C that were associated with signatures of inflammation and T cell activation and were associated with the combination of HLA A*02, B*35 and C*04 alleles suggesting a genetic susceptibility to the development of MIS-C. In a collaboration with the Chertow group evaluated innate immune responses to SARS-CoV-2 in the upper (URT) and lower respiratory tract (LRT) in intubated patients with severe respiratory infections admitted to the ICU in the early phase of the COVID pandemic. We simultaneously assessed expression of type I IFNs (IFNA2 and IFNB1) and Type II IFN (IFNG expression) and the induction of an type-I IFN and NF-B signature in nasopharynx, tracheal aspirates and blood. We compared innate immune responses in the upper respiratory tract (URT) of patients with mild COVID 19 (outpatient) and the hospitalized patients with severe COVID-19. We further characterized the weekly dynamics of these responses in the upper and lower respiratory tracts (LRTs) and in blood for compartmental differences. We observed significantly increased ISG and NF-B responses in the URT of mild compared with severe patients early during illness. This pattern was associated with increased IFNA2 and IFNG expression in the URT of mild patients, a trend toward increased IFNB1-expression and significantly increased STING/IRF3/cGAS expression in the URT of severe patients was seen. By-week across-compartment analysis in severe patients revealed significantly higher ISG responses in the blood compared with the URT and LRT of these patients during the first week of illness, despite significantly lower expression of IFNA2, IFNB1, and IFNG in blood. NF-B responses, however, were significantly elevated in the LRT compared with the URT and blood of severe patients during peak illness (week 2). Our data support that severe COVID-19 is associated with impaired interferon signaling in the URT during early illness and robust pro-inflammatory responses in the LRT during peak illness (Ramos-Benitez MJ et al. medRxiv doi: https://doi.org/10.1101/2022.11.08.22281846).