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Comparison of ILC1s and NK cells transcriptomes in subcutaneous tumor model

ABSTRACT: ILC1s are tissue-resident lymphocytes, their recruitment, migration and infiltration into subcutaneous tumors is a big concern. In addition, as NK cells and ILC1s are phenotypically similar, it is difficult to assess the relative contribution of these two cell types to anti-tumor function. Here, we compared the transcriptomes of ILC1s and NK cells from MC38 tumor-bearing mice to understand the biological/phenotypic changes of ILC1s.

ORGANISM(S): Mus musculus

PROVIDER: GSE253918 | GEO | 2024/08/28

REPOSITORIES: GEO

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The inositol phosphtase INPP4B sustains ILC1s and intratumoral NK cells through an AKT-driven survival pathway

Project description:Innate lymphoid cells (ILCs) are a heterogeneous population of lymphocytes that coordinate early immune responses and maintain tissue homeostasis. Type 1 immune responses are mediated by natural killer (NK) cells and group 1 ILCs (ILC1s). Despite their shared features, NK cells and ILC1s display profound differences among various tissue microenvironments. Here, we identify the inositol polyphosphatase INPP4B as a hallmark feature of tissue-resident ILC1s and intratumoral NK cells using a scRNA-seq atlas of tissue-associated and circulating NK/ILC1s. Conditional deletion of Inpp4b in ILC1s and NK cells reveals that it is necessary for the homeostasis of tissue-resident ILC1s but not circulating NK cells at steady-state. Inpp4b-deficient cells display increased rates of apoptosis and reduced activation of the pro-survival molecule AKT. Furthermore, expression of Inpp4b by NK/ILC1s is necessary for their presence in the intratumoral environment and lack of Inpp4b impairs antitumor immunity. These findings highlight INPP4B as a novel regulator of tissue residency and antitumor function in ILC1s and NK cells.

2024-01-01 | GSE250334 | GEO

Toxoplasma gondii Infection Promotes NK Cell Conversion into ILC1s and Heterogeneous ILC1 Populations

Project description:Innate lymphoid cells (ILCs) comprise several subsets that were originally classified based on their cytokine production profiles. Natural killer (NK) cells and type 1 ILCs (ILC1s) were initially classified together, but recent data supported their separation into different lineages. Here we describe how infection with the parasite Toxoplasma gondii induces changes to NK1.1+ NKp46+ cells that persist independent of ongoing infection. Notably, there is an expansion of Eomes– CD49a+ cells that superficially resemble ILC1s, but express unique genes, circulate throughout the vasculature, and possess distinct epigenetic marks. Single-cell RNA sequencing confirms T. gondii-induced Eomes– CD49a+ cells are distinct from both conventional NK cells and ILC1s. Furthermore, there is heterogeneity within this population, as both conventional NK cells and ILC1s contribute to their formation. Indeed, downregulation of Eomes within conventional NK cells accounts for most T. gondii-induced Eomes– CD49a+ cells, indicating that NK cells can give rise to cells resembling ILC1s during infection.

2019-02-28 | GSE124577 | GEO

Conventional NK cells and ILC1s do not influence pathogenesis of experimental glomerulonephritis

Project description:Innate lymphoid cells (ILCs) that express NK cell receptors (NCRs) and the transcription factor T-bet populate non-lymphoid tissues and are crucial in immune responses against viral infections and malignancies. Recent studies highlighted the heterogeneity of this ILC population and extended their functional spectrum to include important roles in tissue homeostasis and autoimmunity. Here, we provide detailed profiling of NCR+T-bet+ ILC populations in the murine kidney, identifying conventional NK (cNK) cells and type 1 ILCs (ILC1s) as the two major subsets. Induction of renal inflammation in a mouse model of glomerulonephritis did not substantially influence abundance or phenotype of cNK cells or ILC1s in the kidney. For functional analyses in this model, widely used depletion strategies for total NCR+ ILCs (αNK1.1 antibody application) and cNK cells (α-asGM1 serum application) were unreliable tools, since they were accompanied by significant off-target depletion of kidney NKT cells and CD8+ T cells, respectively. However, neither depletion of cNK cells and ILC1s in NKT cell-deficient mice, nor specific genetic deletion of cNK cells in Ncr1Cre/wt x Eomesfl/fl mice altered the clinical course of experimental glomerulonephritis. In summary, we show here that cNK cells and ILC1s are dispensable for initiation and progression of immune-mediated glomerular disease and advise caution in the use of standard antibody depletion methods to study NCR+ ILC function in mouse models.

2022-01-07 | GSE193001 | GEO

Cytotoxic Granzyme C Expressing ILC1s Contribute to Antitumor Immunity and Neonatal Autoimmunity

Project description:Innate lymphocytes are integral components of the cellular immune system that coordinates host defense against a multitude of challenges and can trigger immunopathology when dysregulated. Natural killer (NK) cells and innate lymphoid cells (ILCs) are innate immune effectors postulated to functionally mirror conventional cytotoxic T lymphocytes and helper T cells, respectively. Here, we show that the cytolytic molecule granzyme C was surprisingly expressed in cells with the phenotype of type 1 ILCs (ILC1s) in mouse liver and salivary gland. Cell fate-mapping and transfer studies revealed that granzyme C-expressing innate lymphocytes could be derived from ILC progenitors and did not interconvert with NK cells, ILC2s, or ILC3s. Granzyme C defined a maturation state of ILC1s, which required the transcription factor T-bet and to a lesser extent Eomes specifically in the salivary gland for their maintenance. Furthermore, transforming growth factor-b (TGF-b) signaling promoted maintenance of granzyme C-expressing ILC1s in the salivary gland and in the tumor of a transgenic breast cancer model, and their depletion caused accelerated tumor growth. ILC1s gained granzyme C expression following interleukin-15 (IL-15) stimulation, which enabled perforin-mediated cytotoxicity. Strikingly, constitutive activation of the IL-15-regulated transcription factor Stat5 in granzyme C-fate-mapped ILC1s triggered lethal perforin-dependent autoimmunity in neonatal mice. Thus, granzyme C marks a cytotoxic effector state of ILC1s, broadening their function beyond ‘helper-like’ lymphocytes.

2022-02-18 | GSE196716 | GEO

Gene transcription and chromatin accessibility of conventional NK cells and ILC1s in spleens of uninfected and Toxoplasma gondii-infected Mice

Project description:RNA sequencing and ATAC-seq of conventional NK cells and ILC1s in uninfected mice and mice that were infected 5 wk previously with the Type II Prugniaud strain of T. gondii

2019-05-15 | GSE124313 | GEO

scRNAseq of human blood, tonsil, lung and small intestine innate lymphoid cells

Project description:Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency. Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES− ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7+PRDM1− ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683+ NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.

2024-06-14 | GSE240441 | GEO

RNAseq of macrophages and NK cells from MC38 tumors with PtdSer externalization blockade

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of tumor associated macrophages from WT MC38 tumors and Tmem30a KO tumors; and NK cells from WT and Xkr8 KO MC38 TILs

2022-06-04 | GSE200752 | GEO

Multi-tissue Single-Cell Analysis Deconstructs the Complexities of Mouse NK-ILC1 Programs

Project description:Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1s) are a heterogenous group of T-bet+ innate cells that produce IFN-γ and are broadly defined as lineage–NK1.1+NKp46+ cells in mice. ILC1s definition primarily stems from studies on liver-resident and small intestinal populations. However, ILC1s in many anatomical sites, including visceral adipose tissue, salivary glands, and uterus, exhibit non-uniform programs that do not adequately overlap with those of liver or gut ILC1s or NK cells. Here, we performed single-cell RNA sequencing on murine NK1.1+NKp46+ cells from blood, spleen, lymph nodes, liver, salivary gland, uterus, visceral adipose tissue, small intestines, and several solid tumors. By including cells from an array of niches we defined tissue-specific ILC1 subsets. Moreover, we found a significant heterogeneity of circulating NK cells, due to a spectrum of proliferating, effector and migration programs, which was reduced in tumor-bearing mice, demonstrating repertoire reshaping in response to diseased conditions.

2021-05-04 | GSE158547 | GEO

Conventional NK cells and ILC1s do not influence pathogenesis of experimental glomerulonephritis

Project description:Conventional NK cells and ILC1s do not influence pathogenesis of experimental glomerulonephritis

| PRJNA794113 | ENA

Heterogeneity of liver group 1 ILC1s

Project description:RNA sequencing demonstrated that liver Ly49E+ and Ly49E- ILC1s exhibited unique transcriptional profiles and phenotypic features. scRNA-seq analysis revealed heterogeneity within both cNK and ILC1 subsets in liver. cNK cells could be further divided into three clusters, which corresponded to different developmental stages. Ly49E expression could dissect ILC1s into two subsets: Ly49E+ ILC1s and Ly49E- ILC1s, which exhibited different functional characteristics.

2022-03-27 | GSE171851 | GEO

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