Even mild/moderate COVID-19 infections promote transcriptional reprogramming of the host’s CD14+ monocytes, suggests a new study by Imperial College London, Wellcome Sanger Institute, and Aix Marseille Université in France!
Various changes in the myeloid immune system have been reported in COVID-19, although the particular mechanisms causing these abnormalities are not fully known.
During the acute phase of infection, the researchers evaluated the functioning of traditional CD14+ monocytes as a key myeloid cell component in well-defined cohorts of patients with mild and moderate COVID-19 to as healthy people.
The findings demonstrated that ex vivo isolated CD14+ monocytes from mild and moderate COVID-19 patients have distinct patterns of costimulatory and inhibitory receptors, as well as altered expression of histone marks and a disordered metabolic profile, compared to healthy monocytes.
Notably, it was discovered that lower NFB activation in ex vivo COVID-19 monocytes is associated with an intact type I IFN antiviral response.
In moderate COVID-19 monocytes, pathogen sensing ex vivo resulted in a state of functional unresponsiveness marked by a deficiency in pro-inflammatory cytokine production, NFB-driven cytokine responses, and a faulty type I IFN response.
COVID-19 monocytes shifted their gene expression signature from classical innate immune functions to a pro-thrombotic phenotype defined by elevated expression of hemostasis and immunothrombosis-related pathways.
Monocytes showed abnormalities in the epigenetic remodelling and metabolic reprogramming that normally happens in innate immune cells in response to SARS-CoV-2 or other viral or bacterial components. These data reveal a potential mechanism by which innate immune failure in COVID-19 may contribute to disease pathogenesis.
The researchers investigated the functionality of cluster of differentiation 14-positive (CD14+) monocytes in patients with mild or moderate COVID-19.
COVID-19 respiratory infection is already recognized to cause moderate or subclinical sickness in the majority of people. Moderate to severe disease, on the other hand, is seen in roughly 15% of cases, while critical sickness is seen in 5% of all instances. Myeloid cells, such as monocytes/macrophages, are abundantly concentrated in the lungs of COVID-19 patients during the acute infection phase.
Monocytes are phagocytic, circulating innate immune cells that help detect pathogens and activate innate and adaptive immunity in the face of viral infections.
These monocytes will then differentiate into macrophages and dendritic cells (DCs) in the afflicted tissues, helping to remove pathogens and regenerate tissue.
Various investigations have found that myeloid cells with reduced expression of the human leukocyte antigen (HLA)-DR isoform have dysregulated innate responses to SARS-CoV-2.
In this work, the researchers compared the morphological and functional characteristics of classical (CD14+) monocytes in COVID-19 patients to healthy controls. MHC molecules, as well as costimulatory and coinhibitory receptors, were studied using high-dimensional flow cytometry.
Despite the fact that several global phenotypes were found to overlap between the three groups, monocytes from healthy controls were shown to be unique from those from mild and moderate COVID-19 patients.
“Importantly, monocytes from moderate COVID-19 samples demonstrated reduced expression of HLA-DR,” says Dr. Margarita Dominguez-Villar, Corresponding author of the study, adding “but HLA-ABC expression was elevated relative to mild COVID-19 and control samples.”
“Furthermore,” she adds, “monocytes from moderate COVID-19 samples exhibited reduced expression of CD86, a costimulatory receptor, with an increase in inhibitory receptors – T-cell immunoglobulin and mucin-domain containing-3 (TIM-3) and programmed death-1 (PD-1).”
The researchers discovered 16 distinct monocyte subpopulations (clusters). The cell distribution in each cluster changed between the three groups, demonstrating separate monocyte populations in mild and moderate COVID-19 patients.
The epigenetic marks connected to active transcription, such as H3K27Ac (histone acetylation) and H3K4Me3 (histone methylation), and gene repression, such as H3K9Me2 and H3K27Me3, were studied to investigate gene expression activation or repression patterns.
The researchers discovered that mild COVID-19 monocytes had higher levels of H3K27Ac and H3K4Me3 than controls, but moderate monocytes had expression similar to healthy controls. H3K9Me2, a repressive mark, was not expressed differently; nevertheless, H3K27Me3 expression was elevated in mild COVID-19 monocytes relative to controls, but not in moderate COVID-19 monocytes. These findings revealed that patients with mild COVID-19 had faulty epigenetic remodeling, which led to the activation of innate immune systems.
The researchers compared the gene expression profiles of classical monocytes from moderate COVID-19 patients to healthy controls in depth.
In COVID-19 monocytes, a detailed examination of differential gene expression indicated overexpression of 422 genes and downregulation of 187 genes when compared to healthy patients. Upregulated genes in COVID-19 monocytes exhibited a significant increase in lipid metabolism, interferon (IFN), and cytokine signaling, according to pathway enrichment analysis (PEA).
Ex vivo, increased expression of phopho-IFN regulatory factor 3 (IRF3) and IFN-induced transmembrane protein 2 (IFITM2), an IFN-stimulated gene, validated the elevated type I IFN gene expression in COVID-19 monocytes. PEA analysis of downregulated genes indicated that glycolysis was the sole route that was significantly downregulated in COVID-19 monocytes.
In monocytes from mild COVID-19 patients, the researchers discovered defective metabolic patterns as well as reduced activation of nuclear factor kappa-B (NFB) and intact type I IFN responses.
The ability of monocytes to detect and respond to SARS-CoV-2 ex vivo was next investigated.
After stimulation with SARS-CoV-2, monocytes from healthy controls produced significantly more tumor necrosis factor (TNF) and interleukin (IL)-10.
COVID-19 monocytes, on the other hand, produced less TNF than control monocytes, although IL-10 levels were unaffected. TNF expression was lowered in response to stimulation with bacterial lipopolysaccharide (LPS) or common cold coronaviruses (CoVs), and this was not exclusive to SARS-CoV-2.
Further ribonucleic acid sequencing (RNA-seq) was performed on SARS-CoV-2-activated monocytes from mild COVID-19 patients and healthy controls by the research team.
In COVID-19 monocytes, about 1,437 and 2,073 genes were upregulated and downregulated, respectively, as compared to control monocytes.
Surprisingly, PEA of elevated genes indicated a considerable enrichment of hemostasis and coagulation pathways. Canonical immunological capabilities such as IFN signaling, activation of T cell receptor signaling in T cells, and innate immune functions with non-lymphoid cells were all downregulated in COVID-19 monocytes.
The researchers looked at the metabolic, transcriptomic, and functional aspects of monocytes and discovered various phenotypic and functional abnormalities in COVID-19 patients’ monocytes. When COVID-19 monocytes were exposed to the pathogen, they converted from a classical innate immune function to a pro-thrombotic phenotype.
It was determined that epigenetic and metabolic abnormalities may be at the root of the observed dysfunctional phenotype (in COVID-19 monocytes). For example, the lack of acetyl groups provided by the glycolytic product, acetyl-coenzyme A, could explain the abnormalities in histone acetylation, as glycolysis is greatly downregulated in COVID-19 monocytes.
According to the researchers, more research into the mechanisms that cause monocytic dysfunction is needed. Overall, the findings of the study revealed a method by which innate immune deficiency could contribute to COVID-19 disease.
Source: 10.1101/2022.04.03.486830
Image Credit: Getty
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