Single-cell RNA sequencing of blood antigen-presenting cells in severe Covid-19 reveals multi-process defects in antiviral immunity

AbstractCOVID-19 can lead to life-threatening acute respiratory failure, characterized by simultaneous increase in inflammatory mediators and viral load. The underlying cellular and molecular mechanisms remain unclear. We performed single-cell RNA-sequencing to establish an exhaustive high-resolution map of blood antigen-presenting cells (APC) in 7 COVID-19 patients with moderate or severe pneumonia, at day-1 and day-4 post-admission, and two healthy donors. We generated a unique dataset of 31,513 high quality APC, including monocytes and rare dendritic cell (DC) subsets. We uncovered multiprocess and previously unrecognized defects in anti-viral immune defense in specific APC compartments from severe patients: i) increase of pro-apoptotic genes exclusively in pDC, which are key effectors of antiviral immunity, ii) sharp decrease of innate sensing receptors, TLR7 and DHX9, in pDC and cDC1, respectively, iii) down-regulation of antiviral effector molecules, including Interferon stimulated genes (ISG) in all monocyte subsets, and iv) decrease of MHC class II-related genes, and MHC class II transactivator (CIITA) activity in cDC2, suggesting a viral inhibition of antigen presentation. These novel mechanisms may explain patient aggravation and suggest strategies to restore defective immune defense.

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Single-cell RNA sequencing of blood antigen-presenting cells in severe COVID-19 reveals multi-process defects in antiviral immunity

Nature Cell Biology ◽

10.1038/s41556-021-00681-2 ◽

2021 ◽

Author(s):

Melissa Saichi ◽

Maha Zohra Ladjemi ◽

Sarantis Korniotis ◽

Christophe Rousseau ◽

Zakaria Ait Hamou ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Antigen Presenting Cells ◽

Antiviral Immunity ◽

Single Cell Rna Sequencing ◽

Antigen Presenting

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Abstract 119: Donor Macrophages Modulate Cellular Rejection After Heart Transplantation

Circulation Research ◽

10.1161/res.129.suppl_1.119 ◽

2021 ◽

Vol 129 (Suppl_1) ◽

Author(s):

Benjamin Kopecky ◽

Junedh Amrute ◽

Hao Dun ◽

C. Corbin Frye ◽

DANIEL KREISEL ◽

...

Keyword(s):

T Cells ◽

Heart Transplantation ◽

Single Cell ◽

Rna Sequencing ◽

Expression Profiles ◽

Transplant Rejection ◽

Gene Expression Profiles ◽

Single Cell Rna Sequencing ◽

Monocytes And Macrophages ◽

Antigen Presenting

Heart transplant rejection is common and is associated with significant morbidity and mortality. Current immunosuppressive therapies primarily target recipient T-cells and have a multitude of untoward effects including infections, malignancies, and end-organ damage. Recent studies implicate the roles of antigen presenting cells towards pathogenesis of allograft rejection through recruitment and activation of T-cells. The importance of antigen presenting cell origin, identity, and functional importance remains unknown. Using complimentary imaging and single cell RNA sequencing techniques, we show that donor and recipient monocytes and macrophages co-exist after heart transplantation. These myeloid populations have diverse transcriptional signatures that evolve throughout ongoing rejection. Donor macrophages can be defined ontologically and based on their expression of C-C chemokine receptor 2 (CCR2) and expression of MHC-II. Donor CCR2+ and CCR2- populations can be further defined based on their gene expression profiles, highlighting the marked heterogeneity in the donor macrophage population. Selective depletion of CCR2+ macrophages result in prolonged allograft survival. We use longitudinal single cell RNA sequencing to show that donor CCR2+ and CCR2- macrophages have distinct activation mechanisms such that donor CCR2+ macrophages signal through MyD88/NF-kB. Conditional depletion of MyD88 in donor macrophages recapitulates the donor CCR2+ depletion phenotype. Further interrogation of MyD88 conditionally depleted allografts shows reduced T-cell alloreactivity, holding promise for a potential therapeutic target pathway. Together, we show the molecular identity, diversity, and evolution of donor and recipient monocytes and macrophages as well as the functional relevance and activation pathways of donor macrophages in cardiac allografts.

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Characterization of dendritic cell subtypes in human cord blood by single-cell sequencing

Biophysics Reports ◽

10.1007/s41048-019-00096-5 ◽

2019 ◽

Vol 5 (4) ◽

pp. 199-208

Author(s):

Xiaoyang Jin ◽

Lingyuan Meng ◽

Zhao Yin ◽

Haisheng Yu ◽

Linnan Zhang ◽

...

Keyword(s):

T Cells ◽

Dendritic Cell ◽

Cord Blood ◽

Single Cell ◽

Rna Sequencing ◽

Differential Expression Analysis ◽

Sequencing Data ◽

Human Cord Blood ◽

Single Cell Rna Sequencing ◽

Antigen Presenting

Abstract Dendritic cells (DCs) are professional antigen-presenting cells (APCs). The key functions of DCs include engulfing, processing and presenting antigens to T cells and regulating the activation of T cells. There are two major DC subtypes in human blood: plasmacytoid DCs (pDCs) and conventional DCs. To define the differences between the adult and infant immune systems, especially in terms of DC constitution, we enriched DCs from human cord blood and generated single-cell RNA sequencing data from about 7000 cells using the 10x Genomics Single Cell 3′ Solution. After incorporating the differential expression analysis method in our clustering process, we identified all the known dendritic cell subsets. Interestingly, we also found a group of DCs with gene expression that was a mix of megakaryocytes and pDCs. Further, we verified the expression of selected genes at both the RNA level by PCR and the protein level by flow cytometry. This study further demonstrates the power of single-cell RNA sequencing in dendritic cell research.

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