Dysregulated early transcriptional signatures linked to mast cell and interferon responses are implicated in COVID-19 severity

Abstract

Background: Dysregulated immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are thought to underlie the progression of coronavirus disease 2019 (COVID-19) to severe disease. We sought to determine whether early host immune-related gene expression could predict clinical progression to severe disease.

Methods: We analysed the expression of 579 immunological genes in peripheral blood mononuclear cells taken early after symptom onset using the NanoString nCounter and compared SARS-CoV-2 negative controls with SARS-CoV-2 positive subjects with mild (SARS+ Mild) and Moderate/Severe disease to evaluate disease outcomes. Biobanked plasma samples were also assessed for type I (IFN-α2a and IFN-β), type II (IFN-γ) and type III (IFN-λ1) interferons (IFNs) as well as 10 additional cytokines using multiplex immunoassays.

Results: We identified 19 significantly deregulated genes in 62 SARS-CoV-2 positive subject samples within 5 days of symptom onset and 58 SARS-CoV-2 negative controls and found that type I interferon (IFN) signalling (MX1, IRF7, IFITM1, IFI35, STAT2, IRF4, PML, BST2, STAT1) and genes encoding proinflammatory cytokines (TNF, TNFSF4, PTGS2 and IL1B) were upregulated in both SARS+ groups. Moreover, we found that FCER1, involved in mast cell activation, was upregulated in the SARS+ Mild group but significantly downregulated in the SARS+ Moderate/Severe group. In both SARS+ groups we discovered elevated interferon type I IFN-α2a, type II IFN and type III IFN λ1 plasma levels together with higher IL-10 and IL-6. These results indicate that those with moderate or severe disease are characterised by deficiencies in a mast cell response together with IFN hyper-responsiveness, suggesting that early host antiviral immune responses could be a cause and not a consequence of severe COVID-19.

Conclusions: This study suggests that early host immune responses linking defects in mast cell activation with host interferon responses correlates with more severe outcomes in COVID-19. Further characterisation of this pathway could help inform better treatment for vulnerable individuals.

Keywords: COVID-19; SARS-CoV-2; gene expression; interferon; mast cells; plasma biomarkers.

Figure 1

(A) Comparison of immunological gene expression changes/severe and Mid COVID-19 cases. The horizontal and vertical axes show the logarithmic fold change against negative sample in moderate/severe and mid-cases, respectively. The identity line has been added as guide for genes with similar changes. Genes have colored according to the significance of expression change in both (blue), only in the mid moderate/severe group (red). (B) Comparison of confidence intervals of log2 fold changes in between moderate/severe and mild COVID-19 cases. The vertical axes of panels show the confidence interval of the fold-change and the horizontal axes show the groups. Displayed transcripts are FCER1A, IL1B, TNF, PTGS2, IFIT2, TNFSF4 and PTK2.

Figure 2

Interferon protein levels by COVID-19 disease severity. The distribution of interferon protien levels (A) Type 1 interferon-α2a, (B) Type 1 interferon-β, (C) Type 2 interferon-γ and (D) Type 3 interferon-λ in SAR-CoV-2 Mild and Moderate/Severe groups were compared to patients in the SARS- group. Only significant comparisons are shown: *p<.05, **p<.01, ***p<.001. IFN, Interferon. Bars represent median values shown.

Figure 3

Interleukin protein levels by COVID-19 disease severity. The distribution of interleukin expression (IL-10, IL-12p70, IL-13, IL17-A, IL-2, IL-4, IL-5, IL-6, TNF-alpha, IL-beta) in SRS-Cov-2 mild and severe disease severity groups compared to SASRS-Cov-2 negative patients. NS, no significant. *p<.05, ***p<.001.

Figure 4

Hypothesis of proposed (A) Mast cell activation and (B) IFN-I regulation in early or mild SARS-CoV-2 infection. Mild Sars-CoV-2 infection activates Immunoglobulin E (IgE) receptors on mast celld through FcεR1, the high-affinity receptor for the Fc region of IgE. This triggers an intracellular signalling cascade, leading to de novo production of cytokines and lipid mediators, including TNF, IL-6, CCL2, CCL3, prostaglandin (PG) D2 anf E2, and leukotriene (LK) B4 and C4. This acute inflammatory response stimulates NK cell activation and type I IFN (IFN-α), activation. This leads to induced expression of interferon-stimulated genes (ISGs) via the JAK-STAT signalling pathway and a regulated inflammatory mediator production. Feedback control through IL-4 and IL-10 stimulated autoregulation attenuates a controlled anti-viral response. Hypothesis of proposed (C) Mast cell suppression and (D) IFN-I dysregulation in severe SARS-CoV-2 infection. In severe SARS-CoV-2 disease, in addition to mast cells, other immune cells, particularly Toll-like receptor-expressing T-cells (TLR) 3, 7, and 8, recognises the virus using pathogen recognition receptors (PRRs), attenuating interferon production. In addition, IFNs are secreted in an autocrine and paracrine manner to induce expression of ISGs. This dysregulated phase of SARS-CoV-2 disease sees an amplified innate immunity and high levels of proinflammatory cytokines that results in a sustained cytokine/ chemokine release, termed a "cytokine storm" (28). Reduced IgE activation of FcεR1 by virus, leading to a decrease in mast-cell activation, as well as negative feedback from IL-4 and IL-10, leading to a decrease in overall mast cell activity (29, 30).