Single-cell multi-omics analysis of the immune response in COVID-19
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Abstract
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts ( CD16 + C1QA/B/C + ) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34 + hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8 + T cells and an increased ratio of CD8 + effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.
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SciScore for 10.1101/2021.01.13.21249725: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Brefeldin A (2 μg/mL, GolgiPlug, BD Bioscience, 555029) and anti-CD107a-BB700 antibody (1:50, clone H4A3, BD Bioscience, 566558) was added for additional 4 h into all conditions. anti-CD107a-BB700suggested: NoneSubsequently, cells were washed with PBS, permeabilized with Perm/Wash buffer (BD Biosciences, 554723) according manufacturer’s instruction, and stained with intracellular antibodies for 1 h on ice: anti-IL10-PE (1:10, clone JES3-19F1, BD Biosciences, 559330), anti-IFN-αPC (1:25, Miltenyi Biotec, 130-090-762), anti-TNF-AF700 (1:50, clone MAb11, Biolegend, 502928), anti-IL2-BV421 (1:100, clone … SciScore for 10.1101/2021.01.13.21249725: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Brefeldin A (2 μg/mL, GolgiPlug, BD Bioscience, 555029) and anti-CD107a-BB700 antibody (1:50, clone H4A3, BD Bioscience, 566558) was added for additional 4 h into all conditions. anti-CD107a-BB700suggested: NoneSubsequently, cells were washed with PBS, permeabilized with Perm/Wash buffer (BD Biosciences, 554723) according manufacturer’s instruction, and stained with intracellular antibodies for 1 h on ice: anti-IL10-PE (1:10, clone JES3-19F1, BD Biosciences, 559330), anti-IFN-αPC (1:25, Miltenyi Biotec, 130-090-762), anti-TNF-AF700 (1:50, clone MAb11, Biolegend, 502928), anti-IL2-BV421 (1:100, clone 5344.111, BD Biosciences, 562914), anti-CD154-BV605 (1:50, clone 24-31, Biolegend, 310826). anti-IL10-PEsuggested: Noneanti-IFN-αPCsuggested: Noneanti-TNF-AF700suggested: Noneanti-IL2-BV421suggested: Noneanti-CD154-BV605suggested: NoneSoftware and Algorithms Sentences Resources To assess whether the abundance of cells in each hypersphere are associated with disease status, hypersphere counts were analyzed using the quasi-likelihood (QL) method in edgeR. edgeRsuggested: (edgeR, RRID:SCR_012802)Data were analysed by FlowJo V10 (BD Biosciences). FlowJosuggested: (FlowJo, RRID:SCR_008520)Batch effects were removed across the first 30 PCs using the fastMNN58 implementation in the Bioconductor package batchelor (k=50). Bioconductorsuggested: (Bioconductor, RRID:SCR_006442)Dot plots to visualise marker protein and mRNA expression across clusters were generated using the R package ggplot2. ggplot2suggested: (ggplot2, RRID:SCR_014601)BCR contigs contained in filtered_contigs.fasta and filtered_contig_annotations.csv from all three sites were then pre-processed using immcantion inspired preprocessing pipeline70 implemented in the dandelion python package; dandelion is a novel single cell BCR-seq analysis package for 10x Chromium 5’ data. pythonsuggested: (IPython, RRID:SCR_001658)Constant genes were re-annotated using blastn (v2.10.0+) with CH1 regions of constant gene sequences from IMGT followed by pairwise alignment against curated sequences to correct assignment errors due to insufficient length of constant regions. blastnsuggested: (BLASTN, RRID:SCR_001598)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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