Rewired type I IFN signaling is linked to age-dependent differences in COVID-19
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1130853 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Advanced age is the most important risk factor for severe or even lethal COVID-19, but a thorough understanding of the underlying differences in infection-induced inflammation and cellular pathogenesis is missing. In samples from SARS-CoV-2 infected patients aged 1 to 84 years, we observed a continuous rewiring of type I interferon signaling and signal transducer and activator of transcription (STAT) usage across monocytes, CD4+ T cells and B cells during aging. In vitro investigations using cells from controls confirmed this as a general age-induced phenomenon. Conversion in interferon signaling from STAT1 to STAT3 was associated with increased inflammatory profiles, cytokine release and delayed contraction of infection-induced CD4+ T cells. A shift from solely interferon-responsive germinal center B (GCB) cells towards CD69high GCB and atypical B cells was linked to formation of IgA in children vs complement fixing IgG in adults. Our data provide molecular explanations for inflammation-prone responses to infections during aging.
2025-06-13 | GSE271284 | GEO
Project description:Although most SARS-CoV-2-infected individuals experience mild COVID-19, some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection.
2020-07-06 | GSE149689 | GEO
Project description:We utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. Our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.
2021-03-20 | E-MTAB-10169 | biostudies-arrayexpress
Project description:Autosomal inborn errors of type I IFN immunity and autoantibodies against these cytokines underlie at least 10% of critical COVID-19 pneumonia cases. We report very rare, biochemically deleterious X-linked TLR7 variants in 16 unrelated male individuals aged 7 to 71 years (mean: 36.7 years) from a cohort of 1,202 male patients aged 0.5 to 99 years (mean: 52.9 years) with unexplained critical COVID-19 pneumonia. None of the 331 asymptomatically or mildly infected male individuals aged 1.3 to 102 years (mean: 38.7 years) tested carry such TLR7 variants (p = 3.5 x 10-5). The phenotypes of five hemizygous relatives of index cases infected with SARS-CoV-2 include asymptomatic or mild infection (n=2, 5 and 38 years), or moderate (n=1, 5 years), severe (n=1, 27 years), or critical (n=1, 29 years) pneumonia. Two boys (aged 7 and 12 years) from a cohort of 262 male patients with severe COVID-19 pneumonia (mean: 51.0 years) are hemizygous for a deleterious TLR7 variant. The cumulative allele frequency for deleterious TLR7 variants in the male general population is < 6.5x10-4. We also show that blood B-cell lines and myeloid cell subsets from the patients do not respond to TLR7 stimulation, a phenotype rescued by wild-type TLR7. The patients’ blood plasmacytoid dendritic cells (pDCs) produce low levels of type I IFNs in response to SARS-CoV-2. Overall, X-linked recessive TLR7 deficiency is a highly penetrant genetic etiology of critical COVID-19 pneumonia, in about 1.8% of male patients below the age of 60 years. Human TLR7 and pDCs are essential for protective type I IFN immunity against SARS-CoV-2 in the respiratory tract.
2021-08-11 | GSE181787 | GEO
Project description:The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from non-infected healthy controls. Additionally, low-density granulocytes (LDGs) from patients with severe COVID-19 were included to understand their unique role. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. LDGs from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. These findings underscore the crucial role of neutrophil inflammasomes in driving inflammation during severe COVID-19. The study provides insights into the pathological mechanisms of severe COVID-19 and highlights potential targets for therapeutic intervention.
2024-07-23 | GSE272381 | GEO
Project description:Interferons (IFNs) induced early after SARS-CoV-2 infection are crucial for shaping immunity and preventing severe COVID-19. We previously demonstrated that injection of pegylated interferon-lambda1 (PEG-IFN-λ) accelerated viral clearance in COVID-19 patients. To determine if the viral decline was mediated by enhanced immunity, we assessed in vivo responses to PEG-IFN-λ by single cell RNA sequencing and measured SARS-CoV-2-specific T cell and antibody responses between placebo and PEG-IFN-λ-treated patients. PEG-IFN-λ treatment induced interferon stimulated genes in peripheral immune cells expressing IFNLR1, including plasmacytoid dendritic cells and B cells. PEG-IFN-λ did not affect SARS-CoV-2-specific antibody levels or the magnitude of virus-specific T cells. However, we identified delayed T cell responses in older adults, suggesting that PEG-IFN-λ can overcome delays in adaptive immunity to accelerate viral clearance in high-risk patients. Altogether, PEG-IFN-λ offers an early COVID-19 treatment option for outpatients to boost innate antiviral defenses without dampening peripheral adaptive immunity.
2022-10-14 | GSE215814 | GEO
Project description:Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by significant lung pathology and extrapulmonary complications. Type I interferons (IFNs) play an essential role in the pathogenesis of COVID-19. While rapid induction of type I IFNs limits virus propagation, sustained elevation of type I IFNs in the late phase of the infection is associated with aberrant inflammation and poor clinical outcome. Using proteomic data from a lung-on-chip model revealed that, in addition to macrophages, SARS-CoV-2 infection activates cGAS-STING signalling in endothelial cells through mitochondrial DNA release, leading to cell death and type I IFN production.
2022-04-04 | PXD030753 | Pride
Project description:Although some studies reported the comprehensive mRNA expression analysis of coronavirus disease 2019 (COVID-19) using blood samples to understand its pathogenesis, the characteristics of RNA expression in COVID-19 and sepsis have not been compared. We compared the transcriptome expression of whole blood samples from patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patients with sepsis caused by other bacteria who entered the intensive care unit to clarify the COVID-19-specific RNA expression and understand its pathogenesis. Transcriptomes related to mitochondria were upregulated in COVID-19, whereas those related to neutrophils were upregulated in sepsis. However, the transcriptomes related to neutrophils were upregulated in both COVID-19 and sepsis compared to in healthy controls, whereas the mitochondrial transcriptomes were upregulated in COVID-19 and downregulated in sepsis compared to in healthy controls. Moreover, sepsis showed sub-optimal intrinsic apoptotic features compared with COVID-19. The transcriptome expression of COVID-19 has been examined in vitro but has not been widely validated using human specimens. This study improves the understanding of the pathogenesis of COVID-19 and can contribute to the development of treatments.
2022-11-29 | GSE199816 | GEO
Project description:Using COVID-19 as model, we set out to identify serological, cellular and transcriptomic imprints of pathological responses linked to autoreactive B cells at single-cell resolution
2021-11-02 | E-MTAB-11011 | biostudies-arrayexpress
Project description:To go further insight into the involvement of neutrophils in COVID-19 clinical expression, we performed a proteomic analysis of this blood cell type in COVID-19 patients and two non-infected SARS-CoV-2 control groups composed of healthy subjects and ARDS patients hospitalized in intensive care unit (ICU) respectively. All patients were from Guadeloupe and represent a homogeneous population. We have performed a quantitative proteomic study of neutrophiles from French hot spot COVID region, Guadeloupe, confirming the activation of type I IFN pathway and in some target of IFN as TAP proteins, specifically in COVID patients, but not in hospitalized ARDS non-COVID patients and described modification of the NET proteome potentially associated with ARDS.
2022-07-27 | PXD033293 | Pride