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

严重新冠病毒感染患者的纵向 IFN 特征反应和细胞因子分析

• 批准号: 10927957
• 负责人: Raphaela Goldbach-Mansky
• 金额: $ 1.07万
• 依托单位: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10927957
• 关键词: 2019-nCoV; Acute; Admission activity; Adult; Age Years; Alleles; Antibodies; Autoantibodies; Biological Markers; Blood; Blood specimen; CCL2 gene; COVID-19; COVID-19 pandemic; COVID-19 patient; Cells; Cessation of life; Child; Childhood; China; Clinical; Collaborations; Complication; Conjunctivitis; Data; Development; Disease; Disease Progression; Edema; Emergency Situation; Endothelium; England; Exanthema; Ferritin; Fever; Gelatinase B; Gene Expression Profiling; Genes; Genetic Predisposition to Disease; Genetic Transcription; Homeostasis; Hospitalization; IFNA2 gene; IL18 gene; IRF3 gene; IgG autoantibodies; Immune; Immune system; Impairment; In Vitro; Individual; Infection; Inflammation; Inflammatory Response; Innate Immune Response; Institution; Integration Host Factors; Interferon Type I; Interferon Type II; Interferon alpha; Interferons; Interleukin-1; Interleukin-10; Interleukin-15; Interleukin-2; Interleukin-6; Intubation; LCN2 gene; Leukocytes; Life; Lower respiratory tract structure; Lung diseases; Mediating; Mendelian disorder; Monitor; Mucocutaneous Lymph Node Syndrome; Multisystem Inflammatory Syndrome in Children; NF-kappa B; Nasopharynx; National Institute of Allergy and Infectious Disease; Neutrophil Activation; Organ; Outpatients; Pathologic; Patients; Pattern; Peripheral; Phase; Population; Predisposing Factor; Production; Proteins; RNA; Reporting; Respiratory Tract Infections; Risk Factors; S100A9 gene; SARS coronavirus; SARS-CoV-2 infection; SARS-CoV-2 inhibitor; Sampling; Science; Screening procedure; Serum; Severity of illness; Shock; Signal Pathway; Signal Transduction; Signs and Symptoms; Source; T-Cell Activation; T-Lymphocyte; Time; Tissues; Toxic Shock Syndrome; Trachea; Transcript; Upper respiratory tract; Viral Proteins; Whole Blood; World Health Organization; aspirate; autoinflammatory diseases; cohort; coronavirus disease; cytokine; cytokine release syndrome; diagnostic biomarker; disease-causing mutation; gastrointestinal symptom; genetic signature; heart damage; immune activation; immune modulating agents; inflammatory marker; innate immune pathways; insight; longitudinal analysis; monocyte; mortality; nano-string; pandemic disease; patient subsets; pediatric patients; response; severe COVID-19; systemic inflammatory response; trend

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).

与NIAID COVID联盟合作，我们分析了从84名因严重COVID住院的成人患者中纵向收集的用于RNA分离的全血样本。 我们还评估了来自因严重COVID住院的更大组成年患者（来自布雷西亚n=567，蒙扎77和帕维亚：43）的血清样本的血清IL-18，IL-18 BP和CXCL-9以及从先天性和适应性免疫细胞和/或周围组织释放的spike-2蛋白水平和其他炎症标志物的子集。我们的数据显示，在住院患者中，I型IFN信号传导和NF κ B和II型IFN（IFN γ）调节基因的免疫激活总体降低，但在病情较轻的患者和健康对照中则没有（Abers et al. JCI Insight 2021）。 从28个I型IFN调节基因的分析中得出的转录评分在一个患者亚组中高于健康对照，但COVID-19患者的I型IFN评分显著低于在单基因I型IFN病中观察到的评分。 我们还发现，循环白细胞的IFNA 2的标准化转录水平与蛋白质IFN-2a血液水平不相关。此外，在COVID-19患者中，标准化的IFNA 2转录物仅与28基因I型IFN评分弱相关，这与其他人报道的在COVID-19患者中具有单基因IFN病以及循环浆细胞样DC（pDC）数量减少和循环pDC的I型IFN产生受损的患者中的显著相关性相反（10，16，19）表明COVID患者中IFN α的非造血来源。 对患者首次样本的多变量分析显示，12种生物标志物与系统和单核细胞活化（sTNFRSF 1A、IL-6、CCL 2、铁蛋白、IL-15）、损伤（MMP-9、可溶性ST 2、sST 2）、中性粒细胞活化（NGAL、S100 A9）、内皮活化（sVEGFR 1）和T细胞活化（IL-2）相关，这些与疾病严重程度和死亡率相关。 其中，sST 2，sTNFRSF 1A，IL-10和IL-15在整个住院期间在死亡患者中始终高于那些恢复的患者。（Abers等人，JCI Insight 2020）。 IFN α应答过低导致COVID 19的严重疾病表现。在另一项联合研究中，一个IFN水平特别低，因此受损的患者子集患有危及生命的冠状病毒病2019，在危重疾病发作时，10.2%的队列患者具有针对干扰素（IFN-），13种IFN-或两者的中和免疫球蛋白G（IgG）自身抗体（自身抗体）。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SARS-CoV-2感染者中未发现这些自身抗体。（Bastard et al. Science 2020）。这项研究确定了抗I型IFN抗体的存在作为抑制IFN应答的风险因素，并且与其他宿主因素一起易患严重COVD 19。 一项在急性COVID-19（n=110）和MIS-C（n=76）儿科患者中进行的纵向多机构联合研究，并与儿科健康对照进行比较（pHCs; n=76）显示，急性COVID-19患者具有稳健的I型干扰素（IFN）应答基因特征，而突出的II型IFN依赖性和NF-B依赖性特征，在MIS-C中检测到基质体激活和循环刺突蛋白水平升高，与入院时SARS-CoV-2 PCR状态无关。该研究进一步表明，MIS-C中TRBV 11 -2 T细胞克隆型的短暂扩增与炎症和T细胞活化的特征相关，并且与HLA A*02、B*35和C*04等位基因的组合相关，这表明MIS-C的遗传易感性。 在与Chertow小组的合作中，评估了在COVID大流行早期进入ICU的严重呼吸道感染插管患者的上呼吸道（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I型IFN（IFNA 2和IFNB 1）和II型IFN（IFNG表达）的表达以及鼻咽、气管吸出物和血液中I型IFN和NF-B特征的诱导。 我们比较了轻度COVID-19患者（门诊）和重度COVID-19住院患者的上呼吸道（URT）先天免疫反应。我们进一步描述了这些反应在上呼吸道和下呼吸道（LRT）以及血液中的每周动态，以确定房室差异。我们观察到轻度URT患者的ISG和NF-B反应在疾病早期较重度患者显著增加。这种模式与轻度患者URT中IFNA 2和IFNG表达增加相关，在重度患者URT中观察到IFNB 1表达增加和STING/IRF 3/cGAS表达显著增加的趋势。重症患者的逐周跨室分析显示，在疾病的第一周，与URT和LRT相比，这些患者血液中的ISG反应显著更高，尽管血液中IFNA 2、IFNB 1和IFNG的表达显著更低。然而，在疾病高峰期（第2周），与URT和重症患者的血液相比，LRT中的NF-B反应显著升高。我们的数据支持重度COVID-19与早期疾病期间URT中干扰素信号传导受损和高峰疾病期间LRT中强烈的促炎反应相关（Ramos-Benitez MJ et al. medRxiv doi：https：//doi.org/10.1101/2022.11.08.22281846）。