Expression data from different time points of developing natural killer cells in vitro
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE87787 | GEO | 2017/11/01
SECONDARY ACCESSION(S): PRJNA347621
REPOSITORIES: GEO
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Project description:<p>Natural killer (NK) cells are forced to cope with different oxygen environments even under resting conditions. The adaptation to low oxygen is regulated by oxygen-sensitive transcription factors, the hypoxia-inducible factors (HIFs). The function of HIFs for NK cell activation and metabolic rewiring remains controversial. Activated NK cells are predominantly glycolytic, but the metabolic programs that ensure the maintenance of resting NK cells are enigmatic. By combining <em>in situ</em> metabolomic and transcriptomic analyses in resting murine NK cells, our study defines HIF-1a as a regulator of tryptophan metabolism and cellular nicotinamide adenine dinucleotide (NAD+) levels. The HIF-1a/NAD+ axis prevents ROS production during oxidative phosphorylation (OxPhos) and thereby blocks DNA damage and NK cell apoptosis under steadystate conditions. In contrast, in activated NK cells under hypoxia, HIF-1a is required for glycolysis, and forced HIF-1a expression boosts glycolysis and NK cell performance <em>in vitro</em> and <em>in vivo</em>. Our data highlight two distinct pathways by which HIF-1a interferes with NK cell metabolism. While HIF-1a-driven glycolysis is essential for NK cell activation, resting NK cell homeostasis relies on HIF-1a-dependent tryptophan/NAD+ metabolism.</p><p><br></p><p><strong>Linked cross omic data sets:</strong></p><p>RNA-seq data associated with this study are available in ArrayExpress (BioStudies): accession <a href='https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-12082' rel='noopener noreferrer' target='_blank'>E-MTAB-12082</a>.</p>
2023-06-01 | MTBLS6863 | MetaboLights
Project description:Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells. Liver NK 1.1+CD49+, liver NK 1.1+CD49-, spleen NK 1.1+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads
2014-04-26 | E-GEOD-52043 | biostudies-arrayexpress
Project description:Natural killer (NK) cells belong to the innate immune system where they can control virus infections and developing tumors by cytotoxicity and production of inflammatory cytokines. Most studies of mouse NK cells, however, have focused on conventional NK (cNK) cells found in the spleen. Recently, we described two populations of NK cells within the liver, tissue-resident NK (trNK) cells and those resembling splenic cNK cells. However, the lineage relationship of trNK to cNK cells was unclear because trNK cells display a phenotype associated with immature, developing cNK cells. Moreover, liver trNK cells could be related to thymic NK cells or alternatively, a lineage distinct from both cNK and thymic NK cells. Herein we used detailed transcriptomic, flow cytometric, and functional analysis of mice deficient in several transcription factors to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells, especially because they do not require NFIL3 (E4BP4), the previously described NK cellspecification factor. Analysis of other tissues indicate the presence of trNK cells in skin and uterus with different transcription factor requirements. Thus, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells. Liver DX5-CD49+, liver DX5+CD49-, spleen DX5+ CD49- populations of NK cells were sorted with FACS pooling cells from individual mice to end up with ~100k cells for each samples. mRNA was derived from lysates using Invitrogen oligo-dT beads
2014-04-26 | E-GEOD-52045 | biostudies-arrayexpress
Project description:Natural Killer cells (NK), a major constituent of innate immune system, have the ability to kill the transformed and infected cells without prior sensitization; can be put to immunotherapeutic use against various malignancies. NK cells discriminate between normal cells and transformed cells via a balance of inhibitory and activating signals induced by interactions between NK cell receptors and target cell ligands. Present study investigates whether expansion of NK cells could augment their anti-myeloma (MM) activity. For NK cell expansion, peripheral blood mononuclear cells from healthy donors and myeloma patients were co-cultured with irradiated K562 cells transfected with 4-1BBL and membrane-bound IL15 (K562-mb15-41BBL). A genome-wide profiling approach was performed to identify gene expression signature in expanded NK (ENK) cells and non-expanded NK cells isolated from healthy donors and myeloma patients. A specific set of genes involved in proliferation, migration, adhesion, cytotoxicity, and activation were up regulated post expansion, also confirmed by flow cytometry. Exp-NK cells killed both allogeneic and autologous primary MM cells more avidly than non-exp-NK cells in vitro. Multiple receptors, particularly NKG2D, natural cytotoxicity receptors, and DNAM-1 contributed to target lysis, via a perforin mediated mechanism. In summary, vigorous expansion and high anti-MM activity both in vitro and in vivo provide the rationale for testing exp-NK cells in a clinical trial for high risk MM. Differential gene expression profile in expanded natural killer (ENK) cells and non-expanded natural killer (NK) cells from healthy donors and myeloma patients Eight healthy donor and eight myeloma patients were used in the study. Non-expanded natural killer (NK) cells were isolated from PBMCs of healthy donors and myeloma patients. Expanded natural killer (ENK) cells were generated from same set of samples as mentioned in expansion protocol. All ENK and NK cells were used for gene expression profiling.
2011-03-08 | E-GEOD-27838 | biostudies-arrayexpress
Project description:High levels of the polyunsaturated fatty acid arachidonic acid (AA) in the ovarian carcinoma (OC) microenvironment are associated with short relapse-free survival. OC progression is also linked to impaired immunosurveillance, due in part to dysfunctional natural killer (NK) cells. In the present study, we have combined phosphoproteomics, transcriptional profiling and functional assays to study the impact of AA on NK cell functions. Our data show that AA (i) impairs interleukin-2-mediated NK cell proliferation and pro-inflammatory gene expression by blocking STAT1-dependent signaling, (ii) interferes with NK cell receptor (NCR) signaling, including inhibition of MICA-induced ERK phosphorylation and (iii) affects the production of reactive oxygen species. Intriguingly, low expression of several NK cell receptors is associated with a short survival of OC patients, suggesting that AA, dysfunction of NK cells and OC progression are functionally linked.
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2024-02-20 | MSV000094127 | MassIVE
Project description:V(D)J recombination initiated by recombination-activating gene (RAG) endonucleases is a crucial process for the generation of diversified antigen receptors of T and B lymphocytes but regarded dispensable for the generation of innate natural killer (NK) lymphocytes that lack clonotypic receptors. However, a fraction of human and murine NK cells derives from RAG-expressing progenitors, which have non-productive rearrangements within their Ig and TCR loci. An impact of V(D)J rearrangements on maturation and function of NK cells has been suggested by mouse and human models. We studied the impact of RAG expression ontogeny on NK cell maturation and function by using RAG-fate mapping reporter permanently labeling NK progenitors and mature NK cells.
2025-07-25 | GSE283274 | GEO
Project description:Somatic mutations can lead to the transformation of healthy cells into malignant cells and allow their evasion from immune surveillance. To uncover genes that play a role in the detection and lysis of tumor cells by natural killer (NK) cells, a B lymphoblastoid cell line was subjected to a genome-wide CRISPR screen. Deletion of genes for death receptor and ligands for NK activation receptors was found in cells that survived incubation with primary NK cells. Among the top hits that facilitated NK evasion was SPPL3, a gene for an endoprotease that cleaves transmembrane glycosyl transferases. SPPL3-deficient cells accumulated glycosyl transferases, such as MGAT5, and displayed increased N-glycosylation. Binding of NK receptors NKG2D and CD2 to their corresponding ligands MICB and CD58, and binding of rituximab to CD20, was disrupted. Inhibition of N-glycan maturation restored receptor binding and sensitivity to NK cells. To investigate the cause of this resistant phenotype, a secondary CRISPR screen using a glycosylation-focused library was performed in SPPL3-deficient cells. This screen identified transferases that promote the formation of highly branched N-glycans and N-acetyl-lactosamine (LacNAc) extensions as key regulators that prevent killing. A significant enrichment of poly-LacNAc-containing tetra-antennary species was confirmed by glycoproteomic analysis. These findings provide a basis for understanding why SPPL3 deletions have been linked to cancer.
2024-03-19 | PXD040769 | Pride
Project description:The human cytomegalovirus (HCMV) US12 family consists of ten sequentially arranged genes (US12-21) with poorly characterized function. We now identify novel NK cell evasion functions for four members: US12, US14, US18 and US20. Using a systematic multiplexed proteomics approach to quantify ~1,300 cell surface and ~7,200 whole cell proteins, we demonstrate that the US12 family selectively targets plasma membrane proteins and plays key roles in regulating NK ligands, adhesion molecules and cytokine receptors. US18 and US20 work in concert to suppress cell surface expression of the critical NKp30 ligand B7-H6 thus inhibiting NK cell activation. The US12 family is therefore identified as a major new hub of immune regulation.
2017-02-14 | PXD005883 | Pride
Project description:Natural Killer (NK) cell desensitization induced by persistent stimulation limits durable antitumor immunity, yet the molecular mechanisms governing this dysfunctional state remain poorly defined. To identify conserved regulators of NK cell desensitization, we performed comparative transcriptomic analyses across multiple murine models of persistent activation and dysfunction. We set up multiple robust in vivo and in vitro conditions to compare desensitized NK cells with their functional counterparts. First, we compared functional vs. desensitized NK cells that naturally arise through NK cell education. Normal lymphoid cells lacking MHC I are killed by NK cells, indicating that healthy cells provide stimulatory signals that are normally counterbalanced by inhibitory receptors recognizing self MHC I molecules, such as Kb and Db in C57BL6/J (B6) mice. In B6 mice, these receptors include Ly49C and Ly49I (bind to Kb), and CD94/NKG2A (binds to a Db-derived peptide presented by the Qa-1 nonclassical MHC I molecule). Individual NK cells can express any combination of Ly49C, Ly49I or CD94/NKG2A (abbreviated C, I and N, respectively), or none of them. In B6 mice, NK cells lacking all 3 receptors (C-I-N- NK cells; triple negative, TN) are inhibited the least and therefore persistently stimulated the most by neighboring cells in steady state conditions, resulting in a high degree of desensitization. NK cells expressing only one of the receptors, such as Ly49I+ single positive (SP) cells, are only partially inhibited and therefore less desensitized, and triple positive (TP) NK cells are inhibited the most and therefore least desensitized. Consequently, in response to activating receptor engagement ex vivo, the degranulation and cytokine production responses follow the pattern TP>SP>TN. The same pattern held when we gated on the most mature, CD27-CD11b+ NK cell subset. In MHC I-deficient B2m–/– mice, all NK cells are persistently stimulated and therefore strongly desensitized, similar to TN cells in B6 mice. We next established additional modes of desensitization, including 22-hour stimulation with ionomycin, a calcium ionophore that mimics receptor-induced Ca2+ influx and is known to induce a state of dysfunction in both T cells and NK cells. We confirmed that a 22-hour treatment with ionomycin desensitized murine NK cells. As yet another mode of desensitization, we reproduced persistent ‘induced self’ signals by simultaneously stimulating normal NK cells in vitro via engagement of multiple activating receptors for an extended period. NK cells were desensitized by stimulation for 48-hours with plate-bound antibodies targeting NKp46 in combination with NKG2D or DNAM-1, combinations that optimally activate NK cells. We performed bulk RNA-seq to compare desensitized NK cells and their functional counterparts in the aforementioned conditions: 1) SP vs. TP, TN vs. TP, or TN vs. SP NK cells in B2m+/+ mice (labeled "CIN"), 2) TP NK cells from B2m–/– vs. B2m+/+ mice (B2m), 3) NK cells treated with ionomycin vs. vehicle (iono), and 4) NK cells stimulated for 48 hours with combinations of activating receptor antibodies (Ab combo). Furthermore, in MHC I-deficient tumors, NK cells initially recognize the loss of MHC I and attack tumor cells, such that small tumor loads can be eradicated, but with larger tumor loads NK cells eventually become desensitized and lose the capacity to control the tumors. We further provide gene expression profiles of NK cells isolated from MC38-B2m–/– colorectal tumors as a representation of such case.
2026-07-12 | GSE336796 | GEO
Project description:Natural killer (NK) cells have differential expression of inhibitory and activating receptors. NK cells that express inhibitory receptors with high binding affinity to self are considered licensed and normally functional cells, while those with low affinity are unlicensed are considered hyporesponsive. Microarray analysis was performed to better understand gene expression differences between these two subpopulations of NK cells after culturing the NK cells with IL-2 from splenocytes isolated from C57BL/6 mice and then sorting for CD3-CD122+Ly49G2+Ly49C/I- or CD3-CD122+Ly49G2-Ly49C/I+. Gene fold expression differences were compared between the Ly49G2+ and Ly49C/I+ NK cells to better understand the functional roles and characterisitics of these cells. A total of 6 samples were analyzed, 3 for the CD3-CD122+Ly49G2+Ly49C/I- NK cells and 3 for the CD3-CD122+Ly49G2-Ly49C/I+. Samples were obtained from C57BL/5 splenocytes that were T cells depleted through anti-Thy1.2 and complement mediated depletion and cultured for 7 days with IL-2. Fold changes greater than 1.5 were recorded.
2014-09-01 | E-GEOD-56662 | biostudies-arrayexpress