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Metabolic programs drive function of therapeutic natural killer (NK) cells in low oxygen tumor microenvironments

ABSTRACT: Limited oxygen in solid tumors poses a challenge to successful immunotherapy with NK cells. NK cells have impaired cytotoxicity when cultured in hypoxia (1% oxygen), but not physiologic or atmospheric oxygen (>5%). We sought to analyze the impact of oxygen concentrations on human NK cell biology to determine what factors were driving loss of cytotoxicity and where there were opportunities to overcome hypoxia-induced dysfunction in NK cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE269629 | GEO | 2024/11/06

REPOSITORIES: GEO

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	GSE269629_UMN_NK_counttable.csv.gz	Csv
	GSE269629_countdata_annotated.csv.gz	Csv

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Resting natural killer cell homeostasis relies on tryptophan/NAD+ metabolism and HIF-1α

Project description: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 in situ 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 in vitro and in vivo. 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. Linked cross omic data sets: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>.

2023-06-01 | MTBLS6863 | MetaboLights

Transcriptional Profiling of Hypoxic Neural Stem Cells to Identify Novel Regulators of Neural Stem Cell Biology

Project description:Neural stem cells reside in a hypoxic microenvironment within the brain. However, the crucial transcription factors that regulate neural stem cell biology under physiologic hypoxia are poorly understood. Here, we have performed microarray analysis of hypoxic versus normoxic neural stem cells with the aim of identifying pathways and transcription factors that are activated under oxygen concentrations mimicking normal brain tissue microenvironment. To identify the molecular mechanisms mediating the effect of low oxygen levels on NSC biology, we profiled the global effect of sustained, physiologic hypoxia on NSC gene expression using an unbiased approach by genome-wide microarray analysis. NSC were isolated from E13.5 mouse embryos (OF-1 strain) as previously described (Johe et al., 1996). After isolation, cells were immediately cultured at 37°C, 5% CO2 and either 5% or atmospheric (≈21%) oxygen and maintained in these conditions for 2-3 passages (minimum of 10 days). Then, total RNA was extracted, labeled and hybridized in a SurePrint G3 Mouse GE 8x60k array (Agilent Technologies). Four independent experiments were performed using different mouse donors for each experiment.

2015-07-30 | E-GEOD-68572 | biostudies-arrayexpress

Novel non-canonical role of STAT1 in Natural Killer cell cytotoxicity

Project description:STAT1 is an important regulator of NK cell maturation and cytotoxicity. Although the consequences of Stat1-deficiency have been described in detail the underlying molecular functions of STAT1 in NK cells are only partially understood. Here we describe a novel non-canonical role of STAT1 that was unmasked in NK cells expressing Stat1-Y701F. This mutation prevents JAK-dependent phosphorylation, subsequent nuclear translocation and cytokine-induced transcriptional activity. As expected Stat1-Y701F mice displayed impaired NK cell maturation comparable to Stat1-/- animals. In contrast Stat1-Y701F NK cells exerted a significantly enhanced cytotoxicity in vitro and in vivo suggesting a so-far unknown cytoplasmic function. Using immunofluorescence technology we uncovered the recruitment of STAT1 to the immunological synapse during NK cell killing. A Stat1ind mouse expressing FLAG-tagged STAT1α was used to study the STAT1α interactome in NK cells. Mass spectrometry revealed that STAT1 directly binds proteins involved in cell junction formation and proteins associated to membrane or membrane-bound vesicles. We propose a novel function for STAT1 in the immunological synapse of NK cells regulating tumor surveillance and cytotoxicity.

2016-10-07 | PXD002206 | Pride

ELK3 modulates the antitumor efficacy of natural killer cells against triple negative breast cancer by regulating mitochondrial dynamics [RNA-seq]

Project description:We demostrated that ELK3-Mid51 axis in TNBCs mediate mitochondrial dynamics determines concentration of reactive oxygen species that is linked to the immune sensitivity to cytotoxicity of NK cells.

2022-03-03 | GSE197575 | GEO

ELK3 modulates the antitumor efficacy of natural killer cells against triple negative breast cancer by regulating mitochondrial dynamics [ChIP-seq]

2022-03-03 | GSE197572 | GEO

Short-term hypoxia synergizes with interleukin 15 priming in driving glycolytic gene transcription and supports human natural killer cell activities.

Project description:Natural killer (NK) cells induce apoptosis in infected and transformed cells and produce immunoregulatory cytokines. At this, NK cells operate in inflammatory and tumor environments low in oxygen (hypoxic) and with immunosuppressive properties. In vitro studies of NK cells are, however, commonly performed in ambient air (normoxia). We evaluated the immediate impact of short-term hypoxia on various intrinsic activities of resting and IL-15 primed NK cells and determined underlying transcriptional pathway regulations using a 2 × 2 factorial design. Hypoxia stimulated migration through extracellular matrix, supported secretion of specific chemokines, and shifted amounts of susceptible leukemia target cells toward late apoptosis. IL-15 was a powerful inducer of anabolic gene transcription. Associations of hypoxia with HIF-1 and glycolytic pathways were dependent on priming which represented the largest contrasts observed. Regulatory patterns and RT-PCR validated synergistic hypoxia-IL-15 interactions in upregulation of key glycolytic enzymes suggest an important function for anaerobic glycolysis in priming, underpinning the emerging role of glycolytic switching in driving NK cell function. Adaption to short-term hypoxia appeared however transitory. We conclude that control of oxygen in vitro can promote NK cell features desirable for adoptive transfer therapy.

2016-05-09 | GSE70214 | GEO

Regulation of human granulosa cells by oxygen

Project description:Human granulosa cells (GCs), obtained during medical reproductive procedures can be cultured and are a cellular model for the human ovary. Oxygen concentrations are regarded as important regulators of GCs. We examined consequences of low (1%) O2 versus standard atmospheric conditions in cultured human GCs for four days. A proteomic analysis of three pools of human GCs was performed. While differences between the pools of GCs were noted, the abundance of 133 proteins was significantly increased in hypoxia in all samples, whereas the abundance of 391 proteins was decreased.

2023-12-20 | PXD042934 | Pride

Differential responses of choroidal melanocytes and uveal melanoma cells to low oxygen conditions

Project description:PURPOSE: Tissue culture is traditionally performed at atmospheric oxygen concentration (21%), which induces hyperoxic stress, as endogenous physiologic oxygen tension found in tissues varies between 2% and 9%. This discrepancy may lead to misinterpretation of results and may explain why effects observed in vitro cannot always be reproduced in vivo and vice versa. Only a few studies have been conducted in low physiologic oxygen conditions to understand the development and differentiation of cells from the eye. METHODS: The aim of this study was to investigate the growth and gene expression profile of melanocytes from the choroid permanently exposed to 21% (hyperoxic) or 3% (physiologic) oxygen with proliferation assays and DNA microarray. The cellular behavior of the melanocytes was then compared to that of cancer cells. RESULTS: The gross morphology and melanin content of choroidal melanocytes changed slightly when they were exposed to 3% O2, and the doubling time was statistically significantly faster. There was an increase in the percentage of choroidal melanocytes in the active phases of the cell cycle as observed by using the proliferation marker Ki67. The caveolin-1 senescence marker was not increased in choroidal melanocytes or uveal melanoma cells grown in hyperoxia. In comparison, the morphology of the uveal melanoma cells was similar between the two oxygen levels, and the doubling time was slower at 3% O2. Surprisingly, gene expression profiling of the choroidal melanocytes did not reveal a large list of transcripts considerably dysregulated between the two oxygen concentrations; only the lactate transporter monocarboxylate transporter (MCT4) was statistically significantly upregulated at 3% O2. CONCLUSIONS: This study showed that the oxygen concentration must be tightly controlled in experimental settings, because it influences the subsequent cellular behavior of human choroidal melanocytes.

2016-09-10 | GSE86789 | GEO

Nidogen-1 is a novel extracellular ligand for the NKp44 activating receptor

Project description:The release of soluble ligands of activating Natural Killer (NK) cell receptors may represent a regulatory mechanism of NK cell function both in physiologic and in pathologic conditions. Here, we identified the extracellular matrix protein Nidogen-1 (NID1) as a ligand of NKp44, an important activating receptor expressed by activated NK cells. When released as soluble molecule, NID1 can regulate NK cell function by modulating NKp44-induced IFN-γ production or cytotoxicity. We also show that NID1 may be present at the cell surface. In this form or when bound to a solid support (bNID1), NID1 failed to induce NK cell cytotoxicity or cytokine release. However, analysis by mass spectrometry revealed that exposure to bNID1 can induce relevant changes in the proteomic profiles suggesting an effect on different, biological processes of human NK cells.

2018-10-22 | PXD008252 | Pride

Tissue culture model of hypoxia

Project description:Validation of an in vitro model of hypoxia using a primary cell culture of mouse embryonic fibroblasts (MEF) exposed to 1% oxygen at 37 degrees celsius. Control cells were exposed to atmospheric oxygen.

2014-03-01 | GSE54228 | GEO

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