Transcriptional Changes in CD16+ Monocytes May Contribute to the Pathogenesis of COVID-19

Abstract

The COVID-19 pandemic has caused more than three million deaths globally. The severity of the disease is characterized, in part, by a dysregulated immune response. CD16+ monocytes are innate immune cells involved in inflammatory responses to viral infections, and tissue repair, among other functions. We characterized the transcriptional changes in CD16+ monocytes from PBMC of people with COVID-19, and from healthy individuals using publicly available single cell RNA sequencing data. CD16+ monocytes from people with COVID-19 compared to those from healthy individuals expressed transcriptional changes indicative of increased cell activation, and induction of a migratory phenotype. We also analyzed COVID-19 cases based on severity of the disease and found that mild cases were characterized by upregulation of interferon response and MHC class II related genes, whereas the severe cases had dysregulated expression of mitochondrial and antigen presentation genes, and upregulated inflammatory, cell movement, and apoptotic gene signatures. These results suggest that CD16+ monocytes in people with COVID-19 contribute to a dysregulated host response characterized by decreased antigen presentation, and an elevated inflammatory response with increased monocytic infiltration into tissues. Our results show that there are transcriptomic changes in CD16+ monocytes that may impact the functions of these cells, contributing to the pathogenesis and severity of COVID-19.

Keywords: SARS-CoV-2; cell movement; inflammation; non-classical monocytes; single-cell transcriptomics.

Figure 1

CD16+ monocyte identification and integration analyses. (A) A representative UMAP plot showing identification of CD16+ monocytes based on unsupervised clustering. (B) A UMAP plot after integration of all donor datasets indicate no technical batch effects. COVID-19 samples are shown in purple, and healthy samples in red. (C) UMAP plot showing CD16+ monocytes from severe (blue), mild (purple) and healthy (red) cases.

Figure 2

CD16+ monocytes from COVID-19 samples compared to healthy controls have dysregulated genes related to inflammation and metabolic pathways. (A) A heatmap of the top 20 DEG between CD16+ monocytes from people with COVID-19 and healthy individuals. Each column depicts cells from COVID-19 cases or healthy individuals, and rows indicate the top DEG. The DEG heatmap is colored by normalized gene expression levels. Yellow represents higher expression, and pink represents lower expression. (B, C) IPA of DEG showing the top 10 (B) cellular pathways and (C) diseases and functions predicted to be increased (red) or decreased (blue) in CD16+ monocytes from COVID-19 cases compared to healthy controls. (D) Dot plot of some DEG involved in inflammation between COVID-19 and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene.

Figure 3

Subclustering analysis show similar subpopulations of CD16+ monocytes from COVID-19 and healthy controls. (A) UMAP plot showing subclustering of CD16+ monocytes from COVID-19 cases (left) resulted in similar subpopulations to those found in healthy controls (right). (B) There are similar percentages of cells within the CD16+ subpopulations in COVID-19 samples compared to healthy samples. (C) There are similar percentages of cells within the CD16+ subpopulations in severe and mild COVID-19 samples compared to healthy samples.

Figure 4

CD16+ monocytes from mild cases compared to healthy controls have a strong interferon response. (A) Dot plot of the top 20 DEG between mild cases and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene. Top (B) pathways and (C) diseases and functions predicted to be increased (red) or decreased (blue) in mild cases compared to healthy controls. (D) Dot plot of some DEG involved in oxidative stress response and cell activation between mild cases and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene.

Figure 5

CD16+ monocytes from people with severe COVID-19 compared to healthy controls have upregulated inflammatory and cell movement genes. (A) Dot plot of the top 20 DEG between severe cases and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene. Top (B) pathways and (C) diseases and functions predicted to be increased (red) or decreased (blue) in the severe cases compared to healthy controls. (D) Dot plot of DEG involved in oxidative phosphorylation between mild cases and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene.

Figure 6

CD16+ monocytes from severe cases compared to those from mild cases have dysregulated protein synthesis, antigen presentation, and increased apoptosis related functions. (A) Dot plot of the top 20 DEG between severe and mild cases, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene. Top (B) pathways and (C) diseases and functions predicted to be increased (red) or decreased (blue) in severe cases compared to mild cases. (D) Dot plot of some DEG involved in MSP-RON and T-cell receptor signaling pathways between mild cases and healthy controls, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene.

Figure 7

CD16+ monocytes from the (31) dataset have DEG between COVID-19 and healthy controls that are similar to our dataset. (A) A UMAP plot after integration of donors from the (31) dataset indicate no technical batch effects. COVID-19 samples are shown in purple, and healthy samples in red. (B) A heatmap validating DEG between CD16+ monocytes from people with COVID-19 and healthy individuals. Each column depicts cells from COVID-19 cases or healthy individuals, and rows indicate the top DEG. The DEG heatmap is colored by normalized gene expression levels. Yellow represents higher expression, and pink represents lower expression. (C) UMAP plot showing CD16+ monocytes from severe (blue), mild (purple) and healthy (red) cases. (D) Dot plot validating DEG that we found in this study between mild and healthy cases, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene. (E) Dot plot validating DEG between severe and healthy cases, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene. (F) Dot plot validating DEG between severe and mild cases, represented by a color scale showing lower (blue) to higher (red) gene expression. The size of the dot represents the percentage of cells expressing each specific gene.