Single-Cell Analysis Reveals Macrophage-Driven T Cell Dysfunction in Severe COVID-19 Patients

Authors: Liu et al.

Link to paper: https://doi.org/10.1101/2020.05.23.20100024

Journal/ Pre-Print: medRxiv

Tags: Bioinformatics, Cell Biology, Clinical, Immunology/Immunity, Inflammation

Research Highlights 

1. Macrophages in pleural effusion fluid of 1 severe Covid-19 patient show polarization towards M2-type macrophages.

2. T cells in pleural effusion fluid of 1 severe Covid-19 patient show earlier SARS-CoV2-specific responsivity, increased exhaustion, and high percentage of Tregs, compared to T cells in peripheral blood from the same patient.

3. Sputum macrophages from 2 severe Covid-19 patients showed increased M2 polarization compared to sputum macrophages from 2 mild Covid-19 patients. T cells were not present in these sputum samples

Summary

Liu et al. used single-cell RNA sequencing, flow cytometry and cytokine quantification to analyse leukocytes from pleural effusion (PFMC) and peripheral blood in 1 patient with severe COVID-19 compared to a 2017 dataset from a healthy control. CD4+ and CD8+ T cells in the PFMC expressed increased activation and exhaustion markers compared to PBMC. The monocytes/macrophages in the PFMC expressed high CD163 and CEBPβ, but low CD86, suggesting M2 polarization possibly driving the T cell phenotype. Validation was done with scRNAseq of sputum macrophages: 2 severe patients had higher CD163 and CEBPβ, but lower CD86, than 2 mild patients. This again suggests M2 polarization may correlate with severe Covid-19.

Impact for SARS-CoV2/COVID19 research efforts

Understand the immune response to SARS-CoV2/COVID19

Clinical symptoms and pathogenesis of SARS-Cov2/COVID19

Study Type 

· Patient Case study

Strengths and limitations of the paper

Novelty: It is novel that the authors did not only study PBMC, as in most papers, but also isolated immune cells from the location of the inflammation (pleural effusion, sputum).

Standing in the field: In this study the pleural fluid and sputum macrophages highly express APOE. Literature described a role for APOE in T cell exhaustion, supporting a mechanistic

link between macrophage and T cell phenotypes in this Covid-19 patient. Previous publications report T cells from COVID-19 patients with significantly higher levels of the exhaustion markers (particularly PD-1 and Tim-3) (Bo Diao; Reduction and Functional Exhaustion of T Cells in Patients With Coronavirus Disease 2019 (COVID-19) Front. Immunol., 01 May 2020).

Appropriate statistics: N/A Since most of the paper is about 1 patient, statistical testing was not necessary/possible.

Viral model used: SARS-CoV2 infected patients

Translatability: Not directly translatable, since findings first need to be confirmed by studies with larger patient numbers.

Main limitations: Since only 1 sample of pleural fluid cells and only 4 samples of sputum cells were studied, more samples would be needed to confirm the findings. Currently it cannot be concluded if the patient’s Zadaxin treatment affected the results, as all samples were obtained after starting the treatment. No clinical data provided for 4 out of 5 patients.