A single-cell atlas of the peripheral immune response to severe Covid-19

Authors: Aaron J. Wilk et al.

Link to paper: https://www.medrxiv.org/content/10.1101/2020.04.17.20069930v1

Journal/ Pre-Print: medRxiv

Tags: Bioinformatics, Immunology/Immunity, Inflammation, Molecular biology

Research Highlights 

1. Single cell RNA sequencing of PBMC of 7 Covid-19 patients and 6 healthy controls shows high heterogeneity among patients that could not be linked to clinical characteristics.

2. CD14+ monocytes in Covid-19 patients had decreased HLA-II expression, which could lead to reduced induction of an adaptive immune response.

3. The authors claim to have found a subset of activated granulocytes in ARDS patients that “transdifferentiated” from class-switched B cells. However, the supporting data is very thin, and the transcriptomic signature identifies these cells as a mix of (pro)myelocytes and pre-B cells.

Summary

Single cell RNA sequencing of PBMCs of 7 Covid-19 patients shows high heterogeneity. This could not be linked to clinical characteristics, likely due to the small sample size. ARDS patients (n=4) showed a decreased number of B-cells, CD16+ monocytes, (p)DCs, γδ T-cells, and NK cells, and an increased number of plasmablasts, compared to 6 healthy controls. Non-ventilated patients (n=4) showed decreased γδ T-cells and pDCs, and increased plasmablasts and platelets. In monocytes and NK cells, type I IFN response genes were only increased in 4/7 patients, and pro-inflammatory cytokines were not markedly raised. One patient was sampled longitudinally and showed changes before and after ARDS onset. Although the comparison to HC is unclear, this suggests that circulating leukocytes do not significantly contribute to the potential COVID-19 cytokine storm.

Impact for SARS-CoV2/COVID19 research efforts

Understand the immune response to SARS-CoV2/COVID19

Study Type

· Patient Case study (n = 7, 4 severe/ARDS and 3 moderate)

· In silico study / bioinformatics study

Strengths and limitations of the paper

Novelty: It is interesting to note that only in ARDS patients (pro)myelocytes (neutrophil precursors) were found in PBMCs and not in non-ventilated Covid-19 patients.

Standing in the field: HLA II downregulation in Covid-19 patients has been described before. The notion of B cell “transdifferentiation” to granulocytes is very controversial and insufficiently backed up by data in this paper.

Appropriate statistics: It is unclear in the differential expression analysis whether they corrected the p-value for multiple testing. Sometimes data is only shown in UMAP visualizations and no statistical testing is performed to compare patients vs HC.

Viral model used: SARS-CoV2

Translatability: > Low, the study size is too small to make significant conclusions to uphold translational potential.

> No conserved Ig V gene usage was detected across patient samples.

Main limitations: > Healthy controls are not age/gender/ethnicity matched to the patients.

> Small number of patients (7), very heterogeneous in both clinical characteristics and transcriptome. 5 patients received remdesivir but it’s not disclosed which patients nor whether this affected the PBMC transcriptome.

> Premature conclusions are based on trends in transcriptomic data that are not statistically significant, nor backed up by any other type of data (e.g. proteomics).

> The heatmaps are not appropriately readable.