Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

AbstractType I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

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Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia

eLife ◽

10.7554/elife.69661 ◽

2021 ◽

Vol 10 ◽

Author(s):

Alex R Schuurman ◽

Tom DY Reijnders ◽

Anno Saris ◽

Ivan Ramirez Moral ◽

Michiel Schinkel ◽

...

Keyword(s):

Single Cell ◽

Influenza A ◽

Mononuclear Cells ◽

Single Cell Analysis ◽

Community Acquired Pneumonia ◽

Type I ◽

Cell Analysis ◽

Peripheral Blood Mononuclear ◽

The Common ◽

Peripheral Immune Response

The exact immunopathophysiology of community-acquired pneumonia (CAP) caused by SARS-CoV-2 (COVID-19) remains clouded by a general lack of relevant disease controls. The scarcity of single-cell investigations in the broader population of patients with CAP renders it difficult to distinguish immune features unique to COVID-19 from the common characteristics of a dysregulated host response to pneumonia. We performed integrated single-cell transcriptomic and proteomic analyses in peripheral blood mononuclear cells from a matched cohort of eight patients with COVID-19, eight patients with CAP caused by Influenza A or other pathogens, and four non-infectious control subjects. Using this balanced, multi-omics approach, we describe shared and diverging transcriptional and phenotypic patterns—including increased levels of type I interferon-stimulated natural killer cells in COVID-19, cytotoxic CD8 T EMRA cells in both COVID-19 and influenza, and distinctive monocyte compositions between all groups—and thereby expand our understanding of the peripheral immune response in different etiologies of pneumonia.

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Fractional response analysis reveals logarithmic cytokine responses in cellular populations

Nature Communications ◽

10.1038/s41467-021-24449-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Karol Nienałtowski ◽

Rachel E. Rigby ◽

Jarosław Walczak ◽

Karolina E. Zakrzewska ◽

Edyta Głów ◽

...

Keyword(s):

Single Cell ◽

Mononuclear Cells ◽

Human Peripheral Blood ◽

Cell Types ◽

Response Analysis ◽

Type I ◽

Peripheral Blood Mononuclear ◽

Fractional Response ◽

Different Cell Types ◽

Cell Data

AbstractAlthough we can now measure single-cell signaling responses with multivariate, high-throughput techniques our ability to interpret such measurements is still limited. Even interpretation of dose–response based on single-cell data is not straightforward: signaling responses can differ significantly between cells, encompass multiple signaling effectors, and have dynamic character. Here, we use probabilistic modeling and information-theory to introduce fractional response analysis (FRA), which quantifies changes in fractions of cells with given response levels. FRA can be universally performed for heterogeneous, multivariate, and dynamic measurements and, as we demonstrate, quantifies otherwise hidden patterns in single-cell data. In particular, we show that fractional responses to type I interferon in human peripheral blood mononuclear cells are very similar across different cell types, despite significant differences in mean or median responses and degrees of cell-to-cell heterogeneity. Further, we demonstrate that fractional responses to cytokines scale linearly with the log of the cytokine dose, which uncovers that heterogeneous cellular populations are sensitive to fold-changes in the dose, as opposed to additive changes.

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Fractional response analysis reveals logarithmic cytokine responses in cellular populations

10.1101/2020.12.08.413468 ◽

2020 ◽

Author(s):

Karol Nienałtowski ◽

Rachel E. Rigby ◽

Jarosław Walczak ◽

Karolina E. Zakrzewska ◽

Jan Rehwinkel ◽

...

Keyword(s):

Single Cell ◽

Mononuclear Cells ◽

Human Peripheral Blood ◽

Cell Types ◽

Response Analysis ◽

Type I ◽

Peripheral Blood Mononuclear ◽

Fractional Response ◽

Different Cell Types ◽

Cell Data

ABSTRACTAlthough we can now measure single-cell signaling responses with multivariate, high-throughput techniques our ability to interpret such measurements is still limited. Even interpretation of dose-response based on single-cell data is not straightforward: signaling responses can differ significantly between cells, encompass multiple signaling effectors, and have dynamic character. Here, we use probabilistic modeling and information-theory to introduce fractional response analysis (FRA), which quantifies changes in fractions of cells with given response levels. FRA can be universally performed for heterogeneous, multivariate, and dynamic measurements and, as we demonstrate, uncovers otherwise hidden patterns in single-cell data. In particular, we show that fractional responses to type I interferon in human peripheral blood mononuclear cells are very similar across different cell types, despite significant differences in mean or median responses and degrees of cell-to-cell heterogeneity. Further, we demonstrate that fractional responses to cytokines scale linearly with the log of the cytokine dose, which uncovers that cellular populations are sensitive to fold-changes in the dose, as opposed to additive changes.

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Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19

Science Translational Medicine ◽

10.1126/scitranslmed.abh2624 ◽

2021 ◽

pp. eabh2624

Author(s):

Monique G.P. van der Wijst ◽

Sara E. Vazquez ◽

George C. Hartoularos ◽

Paul Bastard ◽

Tianna Grant ◽

...

Keyword(s):

Peripheral Blood ◽

Mononuclear Cells ◽

Severe Disease ◽

Cell Epitope ◽

Type I Interferons ◽

Type I ◽

Type I Ifn ◽

Peripheral Blood Mononuclear ◽

Immune Alterations ◽

Elevated Expression

Neutralizing autoantibodies against type I interferons (IFNs) have been found in some patients with critical coronavirus disease 2019 (COVID-19), the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the prevalence of these antibodies, their longitudinal dynamics across the disease severity scale, and their functional effects on circulating leukocytes remain unknown. Here, in 284 patients with COVID-19, we found type I IFN-specific autoantibodies in peripheral blood samples from 19% of patients with critical disease and 6% of patients with severe disease. We found no type I IFN autoantibodies in individuals with moderate disease. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 patients with COVID-19 and 26 non-COVID-19 controls revealed a lack of type I IFN-stimulated gene (ISG-I) responses in myeloid cells from patients with critical disease. This was especially evident in dendritic cell populations isolated from patients with critical disease producing type I IFN-specific autoantibodies. Moreover, we found elevated expression of the inhibitory receptor leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) on the surface of monocytes isolated from patients with critical disease early in the disease course. LAIR1 expression is inversely correlated with ISG-I expression response in patients with COVID-19 but is not expressed in healthy controls. The deficient ISG-I response observed in patients with critical COVID-19 with and without type I IFN-specific autoantibodies supports a unifying model for disease pathogenesis involving ISG-I suppression through convergent mechanisms.

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Dynamic blood single-cell immune responses in patients with COVID-19

Signal Transduction and Targeted Therapy ◽

10.1038/s41392-021-00526-2 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Lulin Huang ◽

Yi Shi ◽

Bo Gong ◽

Li Jiang ◽

Zhixin Zhang ◽

...

Keyword(s):

Immune Response ◽

T Lymphocytes ◽

Immune Responses ◽

Single Cell ◽

Mononuclear Cells ◽

Mrna Level ◽

Mitogen Activated Protein Kinase ◽

Interferon Α ◽

Type I ◽

Peripheral Blood Mononuclear

AbstractThe 2019 coronavirus disease (COVID-19) outbreak caused by the SARS-CoV-2 virus is an ongoing global health emergency. However, the virus’ pathogenesis remains unclear, and there is no cure for the disease. We investigated the dynamic changes of blood immune response in patients with COVID-19 at different stages by using 5’ gene expression, T cell receptor (TCR), and B cell receptors (BCR) V(D)J transcriptome analysis at a single-cell resolution. We obtained single-cell mRNA sequencing (scRNA-seq) data of 341,420 peripheral blood mononuclear cells (PBMCs) and 185,430 clonotypic T cells and 28,802 clonotypic B cells from 25 samples of 16 patients with COVID-19 for dynamic studies. In addition, we used three control samples. We found expansion of dendritic cells (DCs), CD14+ monocytes, and megakaryocytes progenitor cells (MP)/platelets and a reduction of naïve CD4+ T lymphocytes in patients with COVID-19, along with a significant decrease of CD8+ T lymphocytes, and natural killer cells (NKs) in patients in critical condition. The type I interferon (IFN-I), mitogen-activated protein kinase (MAPK), and ferroptosis pathways were activated while the disease was active, and recovered gradually after patient conditions improved. Consistent with this finding, the mRNA level of IFN-I signal-induced gene IFI27 was significantly increased in patients with COVID-19 compared with that of the controls in a validation cohort that included 38 patients and 35 controls. The concentration of interferon-α (IFN-α) in the serum of patients with COVID-19 increased significantly compared with that of the controls in an additional cohort of 215 patients with COVID-19 and 106 controls, further suggesting the important role of the IFN-I pathway in the immune response of COVID-19. TCR and BCR sequences analyses indicated that patients with COVID-19 developed specific immune responses against SARS-CoV-2 antigens. Our study reveals a dynamic landscape of human blood immune responses to SARS-CoV-2 infection, providing clues for therapeutic potentials in treating COVID-19.

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Class I–unrestricted noncytotoxic anti–HTLV-I activity of CD8+ T cells

Blood ◽

10.1182/blood.v96.5.1994 ◽

2000 ◽

Vol 96 (5) ◽

pp. 1994-1995 ◽

Cited By ~ 5

Author(s):

Masako Moriuchi ◽

Hiroyuki Moriuchi

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Mononuclear Cells ◽

Membrane Filter ◽

Cd8 T Cell ◽

Class I ◽

Type I ◽

Peripheral Blood Mononuclear ◽

Permeable Membrane

Abstract Although it is widely believed that viral clearance is mediated principally by the destruction of infected cells by cytotoxic T cells, noncytolytic antiviral activity of CD8+ T cells may play a role in preventing the progression to disease in infections with immunodeficiency viruses and hepatitis B virus. We demonstrate here that (1) replication of human T-lymphotropic virus type I (HTLV-I) is more readily detected from CD8+ T-cell–depleted (CD8−) peripheral blood mononuclear cells (PBMCs) of healthy HTLV-I carriers than from unfractionated PBMCs, (2) cocultures of CD8− PBMCs with autologous or allogeneic CD8+ T cells suppressed HTLV-I replication, and (3) CD8+ T-cell anti-HTLV-I activity is not abrogated intrans-well cultures in which CD8+ cells are separated from CD8− PBMCs by a permeable membrane filter. These results suggest that class I-unrestricted noncytolytic anti–HTLV-I activity is mediated, at least in part by a soluble factor(s), and may play a role in the pathogenesis of HTLV-I infection.

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Single-cell multi-omics analysis of the immune response in COVID-19

Nature Medicine ◽

10.1038/s41591-021-01329-2 ◽

2021 ◽

Author(s):

Emily Stephenson ◽

◽

Gary Reynolds ◽

Rachel A. Botting ◽

Fernando J. Calero-Nieto ◽

...

Keyword(s):

Immune Response ◽

T Cells ◽

Single Cell ◽

Mononuclear Cells ◽

Severe Disease ◽

Effector Memory ◽

Peripheral Blood Mononuclear ◽

Cross Sectional ◽

Hematopoietic Stem ◽

Symptomatic Disease

AbstractAnalysis 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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Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma

Respiratory Research ◽

10.1186/s12931-021-01709-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ailu Chen ◽

Maria P. Diaz-Soto ◽

Miguel F. Sanmamed ◽

Taylor Adams ◽

Jonas C. Schupp ◽

...

Keyword(s):

T Cells ◽

Single Cell ◽

Severe Asthma ◽

Mononuclear Cells ◽

Effector T Cells ◽

Poly I:C ◽

Peripheral Blood Mononuclear ◽

Main Cell ◽

Blood Mononuclear Cells ◽

Quantitative Changes

Abstract Background Asthma has been associated with impaired interferon response. Multiple cell types have been implicated in such response impairment and may be responsible for asthma immunopathology. However, existing models to study the immune response in asthma are limited by bulk profiling of cells. Our objective was to Characterize a model of peripheral blood mononuclear cells (PBMCs) of patients with severe asthma (SA) and its response to the TLR3 agonist Poly I:C using two single-cell methods. Methods Two complementary single-cell methods, DropSeq for single-cell RNA sequencing (scRNA-Seq) and mass cytometry (CyTOF), were used to profile PBMCs of SA patients and healthy controls (HC). Poly I:C-stimulated and unstimulated cells were analyzed in this study. Results PBMCs (n = 9414) from five SA (n = 6099) and three HC (n = 3315) were profiled using scRNA-Seq. Six main cell subsets, namely CD4 + T cells, CD8 + T cells, natural killer (NK) cells, B cells, dendritic cells (DCs), and monocytes, were identified. CD4 + T cells were the main cell type in SA and demonstrated a pro-inflammatory profile characterized by increased JAK1 expression. Following Poly I:C stimulation, PBMCs from SA had a robust induction of interferon pathways compared with HC. CyTOF profiling of Poly I:C stimulated and unstimulated PBMCs (n = 160,000) from the same individuals (SA = 5; HC = 3) demonstrated higher CD8 + and CD8 + effector T cells in SA at baseline, followed by a decrease of CD8 + effector T cells after poly I:C stimulation. Conclusions Single-cell profiling of an in vitro model using PBMCs in patients with SA identified activation of pro-inflammatory pathways at baseline and strong response to Poly I:C, as well as quantitative changes in CD8 + effector cells. Thus, transcriptomic and cell quantitative changes are associated with immune cell heterogeneity in this model to evaluate interferon responses in severe asthma.

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The 2′-O-methylation status of a single guanosine controls transfer RNA–mediated Toll-like receptor 7 activation or inhibition

Journal of Experimental Medicine ◽

10.1084/jem.20111075 ◽

2012 ◽

Vol 209 (2) ◽

pp. 235-241 ◽

Cited By ~ 61

Author(s):

Stefanie Jöckel ◽

Gernot Nees ◽

Romy Sommer ◽

Yang Zhao ◽

Dmitry Cherkasov ◽

...

Keyword(s):

Influenza A ◽

Mononuclear Cells ◽

Human Peripheral Blood ◽

Thermus Thermophilus ◽

Methylation Status ◽

Transfer Rna ◽

Type I ◽

Peripheral Blood Mononuclear ◽

Molecular Pattern

Foreign RNA serves as pathogen-associated molecular pattern (PAMP) and is a potent immune stimulator for innate immune receptors. However, the role of single bacterial RNA species in immune activation has not been characterized in detail. We analyzed the immunostimulatory potential of transfer RNA (tRNA) from different bacteria. Interestingly, bacterial tRNA induced type I interferon (IFN) and inflammatory cytokines in mouse dendritic cells (DCs) and human peripheral blood mononuclear cells (PBMCs). Cytokine production was TLR7 dependent because TLR7-deficient mouse DCs did not respond and TLR7 inhibitory oligonucleotides inhibited tRNA-mediated activation. However, not all bacterial tRNA induced IFN-α because tRNA from Escherichia coli Nissle 1917 and Thermus thermophilus were non-immunostimulatory. Of note, tRNA from an E. coli knockout strain for tRNA (Gm18)-2′-O-methyltransferase (trmH) regained immunostimulatory potential. Additionally, in vitro methylation of this immunostimulatory Gm18-negative tRNA with recombinant trmH from T. thermophilus abolished its IFN-α inducing potential. More importantly, Gm18-modified tRNA acted as TLR7 antagonist and blocked IFN-α induction of influenza A virus–infected PBMCs.

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