Immune system cells from COVID-19 patients display compromised mitochondrial-nuclear expression co-regulation and rewiring toward glycolysis

Abstract

Mitochondria are pivotal for bioenergetics, as well as in cellular response to viral infections. Nevertheless, their role in COVID-19 was largely overlooked. Here, we analyzed available bulk RNA-seq datasets from COVID-19 patients and corresponding healthy controls (three blood datasets, N = 48 healthy, 119 patients; two respiratory tract datasets, N = 157 healthy, 524 patients). We found significantly reduced mtDNA gene expression in blood, but not in respiratory tract samples from patients. Next, analysis of eight single-cells RNA-seq datasets from peripheral blood mononuclear cells, nasopharyngeal samples, and Bronchoalveolar lavage fluid (N = 1,192,243 cells), revealed significantly reduced mtDNA gene expression especially in immune system cells from patients. This is associated with elevated expression of nuclear DNA-encoded OXPHOS subunits, suggesting compromised mitochondrial-nuclear co-regulation. This, together with elevated expression of ROS-response genes and glycolysis enzymes in patients, suggest rewiring toward glycolysis, thus generating beneficial conditions for SARS-CoV-2 replication. Our findings underline the centrality of mitochondrial dysfunction in COVID-19.

Keywords: Genomics; Immune system; Virology.

Graphical abstract

Figure 1

Workflow of this study Several different publicly available bulk and single-cell RNA-seq datasets from healthy and COVID-19 patients were obtained for analysis (see Table 1 for resources). For scRNA-seq data quality control, cells were filtered to retain only those with read counts in mtDNA encoded-protein genes. Finally, differential expression analysis of mitochondrial genes was performed. ∗Dataset III was used both for bulk and scRNA RNA-seq analyses, and hence was considered two separate datasets.

Figure 2

Decreased mtDNA gene expression levels as a feature of COVID-19 in peripheral blood (A) Box plot of bulk RNA-seq analysis in peripheral blood displays lower mtDNA gene expression in COVID-19 patients as compared to healthy controls (Dataset II). (B) Box plot displaying mtDNA gene expression across COVID-19 pseudotimes as compared to control (Dataset III – bulk RNA-seq). X axis – mtDNA genes, Y axis – normalized read counts, which account for expression levels. Significance: ∗ - p < 0.05, ∗∗ - p < 0.005, ∗∗∗ - p < 0.0005. See also Figures S1 and S2 and Table S1.

Figure 3

Expression of nuclear DNA genes involved in mitochondrial function or regulation of mitochondrial gene expression was consistently altered in peripheral blood from patients (A) Heatmaps of significant differentially expressed genes in mitochondria-related biochemical pathways. Color bar representing the log-fold-change (logFC) of significant and consistent genes' expression in COVID-19 patients. Genes with logFC higher than 0.2 or less than −0.2 are shown. Red: positive logFC, purple: negative logFC. (B) Box plots of GAPDH, LDHA and LDHB and (C) JUND, JUN (i.e., c-Jun), POLRMT expression levels in Datasets II (left panel) and Dataset III- bulk RNA-seq (right panel) (see Figure S2 for Dataset V). X axis – gene names; Y axis – normalized read counts as in Figure 2. Significance: ∗ - p < 0.05, ∗∗ - p < 0.005, ∗∗∗ - p < 0.0005. See also Figure S2 and Tables S2 and S3 (https://doi.org/10.17632/8kd3xjfrh4.1).

Figure 4

The change in mtDNA genes expression in COVID-19 patients varies among cell types, and is more prominent in immune system cells (A) Box Plots of mtDNA gene expression from healthy and COVID-19 patients in (i) CD8 T BALF cells (Dataset VI), (ii) CD8 T memory PBMC cells (Dataset VII), (iii) NK BALF cells (Dataset VI) (iv) Ciliated NP cells (Dataset VIII). X axis - gene names; Y axis – normalized UMI (unique molecular identifier) counts. (B) Bar plot presenting the fraction of significantly altered mtDNA genes' expression per cell type. X axis: cell types present in at least two datasets, Y axis: fraction of mtDNA genes with significantly altered expression. Orange - Epithelial cells, Green – Immune system cells. Dataset numbers are indicated in parenthesis. The dashed line represents a threshold of significance in half of the analyzed mtDNA genes. See also Tables S1 and S4 (https://doi.org/10.17632/8kd3xjfrh4.1).