Intra-lineage Plasticity and Functional Reprogramming Maintain Natural Killer Cell Repertoire Diversity

AbstractNatural killer (NK) cell repertoires are made up of a vast number of phenotypically distinct subsets with different functional properties. The molecular programs involved in maintaining NK cell repertoire diversity under homeostatic conditions remains elusive. Here we show that subset-specific NK cell proliferation kinetics correlate with mTOR activation, and that global repertoire diversity is maintained through a high degree of intra-lineage subset plasticity during IL-15-driven homeostatic proliferation in vitro. High-resolution flow cytometry and single cell RNA sequencing revealed that slowly cycling sorted KIR+CD56dim NK cells with an induced CD57 phenotype display increased functional potential associated with inhibitory MHC interactions and activating DAP12 signaling. In contrast, rapidly cycling cells upregulate NKG2A and display a general loss of functionality associated with a transcriptional increase in RNA-binding metabolic enzymes and cytokine signaling pathways. These results shed new light on the role of intra-lineage plasticity during NK cell homeostasis and suggest that the functional fate of the cell is tightly linked to the acquired phenotype and determined by transcriptional reprogramming.One Sentence Summary:High-resolution flow cytometry combined with single-cell RNA sequencing reveal a role for intra-lineage plasticity and functional reprogramming in maintaining phenotypically and functionally diverse NK cell repertoires during IL-15-driven homeostatic proliferation.

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Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia

Cellular and Molecular Immunology ◽

10.1038/s41423-020-00574-8 ◽

2020 ◽

Author(s):

Adeline Crinier ◽

Pierre-Yves Dumas ◽

Bertrand Escalière ◽

Christelle Piperoglou ◽

Laurine Gil ◽

...

Keyword(s):

Bone Marrow ◽

Acute Myeloid Leukemia ◽

Nk Cells ◽

Single Cell ◽

Natural Killer ◽

Rna Sequencing ◽

Myeloid Leukemia ◽

Nk Cell ◽

Single Cell Rna Sequencing ◽

Acute Myeloid

SummaryNatural killer (NK) cells are innate cytotoxic lymphoid cells (ILCs) involved in the killing of infected and tumor cells. Among human and mouse NK cells from the spleen and blood, we previously identified by single-cell RNA sequencing (scRNAseq) two similar major subsets, NK1 and NK2. Using the same technology, we report here the identification, by single-cell RNA sequencing (scRNAseq), of three NK cell subpopulations in human bone marrow. Pseudotime analysis identified a subset of resident CD56bright NK cells, NK0 cells, as the precursor of both circulating CD56dim NK1-like NK cells and CD56bright NK2-like NK cells in human bone marrow and spleen under physiological conditions. Transcriptomic profiles of bone marrow NK cells from patients with acute myeloid leukemia (AML) exhibited stress-induced repression of NK cell effector functions, highlighting the profound impact of this disease on NK cell heterogeneity. Bone marrow NK cells from AML patients exhibited reduced levels of CD160, but the CD160high group had a significantly higher survival rate.

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Cell subtypes and immune dysfunction in peritoneal fluid of endometriosis revealed by single-cell RNA-sequencing

Cell & Bioscience ◽

10.1186/s13578-021-00613-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gen Zou ◽

Jianzhang Wang ◽

Xinxin Xu ◽

Ping Xu ◽

Libo Zhu ◽

...

Keyword(s):

Dendritic Cells ◽

Single Cell ◽

Natural Killer ◽

Rna Sequencing ◽

Peritoneal Cavity ◽

Immune Cells ◽

Peritoneal Fluid ◽

Control Sample ◽

Immune Dysfunction ◽

Single Cell Rna Sequencing

Abstract Background Endometriosis is a refractory and recurrent disease and it affects nearly 10% of reproductive-aged women and 40% of infertile patients. The commonly accepted theory for endometriosis is retrograde menstruation where endometrial tissues invade into peritoneal cavity and fail to be cleared due to immune dysfunction. Therefore, the comprehensive understanding of immunologic microenvironment of peritoneal cavity deserves further investigation for the previous studies mainly focus on one or several immune cells. Results High-quality transcriptomes were from peritoneal fluid samples of patients with endometriosis and control, and firstly subjected to 10 × genomics single-cell RNA-sequencing. We acquired the single-cell transcriptomes of 10,280 cells from endometriosis sample and 7250 cells from control sample with an average of approximately 63,000 reads per cell. A comprehensive map of overall cells in peritoneal fluid was first exhibited. We unveiled the heterogeneity of immune cells and discovered new cell subtypes including T cell receptor positive (TCR+) macrophages, proliferating macrophages and natural killer dendritic cells in peritoneal fluid, which was further verified by double immunofluorescence staining and flow cytometry. Pseudo-time analysis showed that the response of macrophages to the menstrual debris might follow the certain differentiation trajectory after endometrial tissues invaded into the peritoneal cavity, that is, from antigen presentation to pro-inflammation, then to chemotaxis and phagocytosis. Our analyses also mirrored the dysfunctions of immune cells including decreased phagocytosis and cytotoxic activity and elevated pro-inflammatory and chemotactic effects in endometriosis. Conclusion TCR+ macrophages, proliferating macrophages and natural killer dendritic cells are firstly reported in human peritoneal fluid. Our results also revealed that immune dysfunction happens in peritoneal fluid of endometriosis, which may be responsible for the residues of invaded menstrual debris. It provided a large-scale and high-dimensional characterization of peritoneal microenvironment and offered a useful resource for future development of immunotherapy.

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Single-Cell RNA Sequencing Reveals the Expansion of Cytotoxic CD4+ T Lymphocytes and a Landscape of Immune Cells in Primary Sjögren’s Syndrome

Frontiers in Immunology ◽

10.3389/fimmu.2020.594658 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xiaoping Hong ◽

Shuhui Meng ◽

Donge Tang ◽

Tingting Wang ◽

Liping Ding ◽

...

Keyword(s):

Flow Cytometry ◽

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cell ◽

Susceptibility Genes ◽

Primary Sjögren’S Syndrome ◽

Healthy Controls ◽

Immune Cell Subsets ◽

Single Cell Rna Sequencing

ObjectivePrimary Sjögren’s syndrome (pSS) is a systemic autoimmune disease, and its pathogenetic mechanism is far from being understood. In this study, we aimed to explore the cellular and molecular mechanisms that lead to pathogenesis of this disease.MethodsWe applied single-cell RNA sequencing (scRNA-seq) to 57,288 peripheral blood mononuclear cells (PBMCs) from five patients with pSS and five healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed. Flow cytometry was preformed to verify the result of scRNA-seq.ResultsWe identified two subpopulations significantly expand in pSS patients. The one highly expressing cytotoxicity genes is named as CD4+ CTLs cytotoxic T lymphocyte, and another highly expressing T cell receptor (TCR) variable gene is named as CD4+ TRAV13-2+ T cell. Flow cytometry results showed the percentages of CD4+ CTLs, which were profiled with CD4+ and GZMB+ staining; the total T cells of 10 patients with pSS were significantly higher than those of 10 healthy controls (P= 0.008). The expression level of IL-1β in macrophages, TCL1A in B cells, as well as interferon (IFN) response genes in most cell subsets was upregulated in the patients with pSS. Susceptibility genes including HLA-DRB5, CTLA4, and AQP3 were highly expressed in patients with pSS.ConclusionsOur data revealed disease-specific immune cell subsets and provided some potential new targets of pSS. Specific expansion of CD4+ CTLs may be involved in the pathogenesis of pSS, which might give valuable insights for therapeutic interventions of pSS.

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Natural Killer Cell Diversity in Viral Infection: Why and How Much?

Pathogens and Immunity ◽

10.20411/pai.v1i1.142 ◽

2016 ◽

Vol 1 (1) ◽

pp. 165 ◽

Cited By ~ 9

Author(s):

Catherine A. Blish

Keyword(s):

Natural Killer ◽

Cell Function ◽

Nk Cell ◽

Expression Patterns ◽

Killer Cell ◽

Inhibitory Receptors ◽

Cell Repertoire ◽

Cell Diversity ◽

Repertoire Diversity ◽

Functional Consequences

Natural killer cells are a diverse group of innate lymphocytes that are specialized to rapidly respond to cancerous or virus-infected cells. NK cell function is controlled by the integration of signals from activating and inhibitory receptors expressed at the cell surface. Variegated expression patterns of these activating and inhibitory receptors at the single cell level leads to a highly diverse NK cell repertoire. Here I review the factors that influence NK cell repertoire diversity and its functional consequences for our ability to fight viruses.

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Single-Cell RNA Sequencing of Tumor-Infiltrating NK Cells Reveals that Inhibition of Transcription Factor HIF-1α Unleashes NK Cell Activity

Immunity ◽

10.1016/j.immuni.2020.05.001 ◽

2020 ◽

Vol 52 (6) ◽

pp. 1075-1087.e8 ◽

Cited By ~ 7

Author(s):

Jing Ni ◽

Xi Wang ◽

Ana Stojanovic ◽

Qin Zhang ◽

Marian Wincher ◽

...

Keyword(s):

Transcription Factor ◽

Nk Cells ◽

Single Cell ◽

Rna Sequencing ◽

Nk Cell ◽

Cell Activity ◽

Nk Cell Activity ◽

Single Cell Rna Sequencing

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Single-cell RNA-sequencing reveals profound changes in circulating immune cells in patients with heart failure

Cardiovascular Research ◽

10.1093/cvr/cvaa101 ◽

2020 ◽

Cited By ~ 3

Author(s):

Wesley T Abplanalp ◽

David John ◽

Sebastian Cremer ◽

Birgit Assmus ◽

Lena Dorsheimer ◽

...

Keyword(s):

Heart Failure ◽

Flow Cytometry ◽

Single Cell ◽

Rna Sequencing ◽

Immune Cells ◽

Healthy Subjects ◽

Patients With Heart Failure ◽

Single Cell Rna Sequencing ◽

The Impact ◽

Classical Monocytes

Abstract Aims Identification of signatures of immune cells at single-cell level may provide novel insights into changes of immune-related disorders. Therefore, we used single-cell RNA-sequencing to determine the impact of heart failure on circulating immune cells. Methods and results We demonstrate a significant change in monocyte to T-cell ratio in patients with heart failure, compared to healthy subjects, which were validated by flow cytometry analysis. Subclustering of monocytes and stratification of the clusters according to relative CD14 and FCGR3A (CD16) expression allowed annotation of classical, intermediate, and non-classical monocytes. Heart failure had a specific impact on the gene expression patterns in these subpopulations. Metabolically active genes such as FABP5 were highly enriched in classical monocytes of heart failure patients, whereas β-catenin expression was significantly higher in intermediate monocytes. The selective regulation of signatures in the monocyte subpopulations was validated by classical and multifactor dimensionality reduction flow cytometry analyses. Conclusion Together this study shows that circulating cells derived from patients with heart failure have altered phenotypes. These data provide a rich source for identification of signatures of immune cells in heart failure compared to healthy subjects. The observed increase in FABP5 and signatures of Wnt signalling may contribute to enhanced monocyte activation.

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