Circulating monocytes expressing senescence-associated features are enriched in COVID-19 patients with severe disease

Abstract

Accurate biomarkers for predicting COVID-19 severity have remained an unmet need due to an incomplete understanding of virus pathogenesis and heterogeneity among patients. Cellular senescence and its pro-inflammatory phenotype are suggested to be a consequence of SARS-CoV-2 infection and potentially drive infection-dependent pathological sequelae. Senescence-associated markers in infected individuals have been identified primarily in the lower respiratory tract, while little is known about their presence in more easily accessible bio-specimens. Here, we measured the abundance of senescence-associated signatures in whole blood, plasma and peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and patients without an infection. Bulk transcriptomic and targeted proteomic assays revealed that the level of senescence-associated markers, including the senescence-associated secretory phenotype (SASP), is predictive of SARS-CoV-2 infection. Single-cell RNA-sequencing data demonstrated that a senescence signature is particularly enriched in monocytes of COVID-19 patients, partially correlating with disease severity. Our findings suggest that monocytes are prematurely induced to senescence by SARS-CoV-2 infection, might contribute to exacerbating a SASP-like inflammatory response and can serve as markers and predictors for COVID-19 and its sequelae.

Keywords: COVID-19; SARS-CoV-2; SASP; ageing; cellular senescence; monocytes.

FIGURE 1

Whole blood transcriptome and plasma SASPs showed senescent signatures in COVID‐19 patients. (a) Heatmap of SASP proteins identified in plasma samples from healthy donors (green), patients with non‐severe symptoms (yellow) and patients with severe symptoms (tangerine). (b). Principal component analysis plot that shows the clustering of RNA‐Seq samples based on their gene expression levels. (c) Dot plot of the top 15 enriched GO terms based on the differentially expressed genes in non‐severe and severe patients when compared to control individuals. (d) Expression levels of the CDKN1A gene in relation to the severity of the disease. (e) Heatmap analysis of the SenMayo gene signature.

FIGURE 2

Identification of monocytes as the primary source of senescence in COVID‐19 patients, as evidenced by the up‐regulation of CDKN1A. (a) Uniform Manifold Approximation and Projection (UMAP) plot representing the identified cell types. (b) UMAP plot showing the expression of senescent marker gene CDKN1A in all cell types. The colour is labelled based on the expression level in log scale. (c) CDKN1A expression in monocytes. (d) Cell cycle position density plot for monocytes from samples with different disease severity. (E, F) Area under the curve (AUC) scores of the SenMayo gene list in monocytes (e), with a specific focus on the AUC scores of CDKN1A positive and negative monocyte cells (f). (g) UMAP plot of cell annotation results and expression levels of the senescent markers CDKN1A and CD36. The log‐normalized gene expression levels are represented by a colour scale. (h) Expression levels of CDKN1A and CD36 associated with disease severity. WHO severity categories include HV: Healthy Volunteer; COVID_MILD: COVID patient with mild symptoms; COVID_SEV: COVID patient with severe symptoms; COVID_CRIT: COVID patient with critical symptoms.