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CITE-seq of in vitro control and memory-like human NK cells

ABSTRACT: CITE-seq of in vitro control and memory-like human NK cells

PROVIDER: PRJNA771661 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16355693_1.fastq.gz	Fastqsanger.gz
	SRR16355693_2.fastq.gz	Fastqsanger.gz
	SRR16355694_1.fastq.gz	Fastqsanger.gz
	SRR16355694_2.fastq.gz	Fastqsanger.gz
	SRR16355695_1.fastq.gz	Fastqsanger.gz

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CITE-seq of in vitro control and memory-like human NK cells

Project description:Peripheral blood NK cells were cultured into either control or cytokine-induced memory-like NK cells as described in PMID: 32614951. After differentiation, cells were labeled with hashtag antibodies and cite-seq antibodies and control and memory-like NK cells were combined and loaded onto the 10x Genomics Chromium Instrument a the McDonnell Genome Institute at Washington University School of Medicine. The following samples were analyzed to develop a classification tool for unbiased identification of memory-like NK cells in a bulk single-cell RNA-seq population.

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Project description:NK cells from healthy donors were isolated from peripheral blood and stimulated overnight with IL-12/15/18 to induce a memory-like phenotype. After 7 days of culture, the phenotype and degranulation potential of CIML NK cells was characterized in two distinct NK cell subsets: CD16+/CD56+ and CD16−/CD56. Finally, NK cell subsets were purified using fluorescence-activated cell sorting (FACS) and subjected to high-throughput multiplexed quantitative proteomics.

2025-07-14 | PXD059190 | Pride

Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq]

Project description:NK cells are innate lymphoid cells that protect the host against malignant and infected cells. Activation with the cytokines IL-12, IL-15, and IL-18 induces NK cells to differentiate into memory-like NK cells that have enhanced function compared to conventional NK (cNK) cells. However, mechanisms governing their biology and whether all cNK cells become memory-like are unclear. We identified that IL-12/15/18 activation results in two main fates: reprogramming into enriched memory-like (eML) or priming into effector (eff)cNK cells. eML NK cells have distinct epigenetics, phenotype, and enhanced function (IFNγ, cytotoxicity) compared to cNK and effcNK cells. In contrast, effcNK cells transcriptionally and epigenetically resemble cNK cells. Furthermore, we identify that within cNK cells CD56bright and CD56dim NK cells are the origin of distinct subsets of eML NK cells. Moreover, these two subsets of eML NK cells persist within patients receiving ML NK cell therapy for several months. Thus, IL-12/15/18 activation of NK cells results in multiple cell fates, with epigenetic and transcriptional mechanisms orchestrating eML NK cell differentiation and function. These mechanistic insights provide new strategies to enhance NK cellular therapy.

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RNA expression of memory NK subsets

Project description:we compared and reported RNA expression difference in memory and non-memory NK cell subsets

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CITE-seq of CAR-NK cells

Project description:Primary chimeric antigen receptor (CAR) natural killer (NK) cells show strong cytotoxic efficacy against acute myeloid leukemia (AML) in vivo. However, NK cell-mediated tumor killing is often impaired by tumor-mediated immune cell inactivation. Here, we report a novel strategy to overcome NK cell inhibition caused by the immune checkpoint NKG2A, which interacts with HLA-E expressed on AML blasts. We generated AML-specific CD33-directed CAR (CAR33)-KLRC1ko-NK cells with CRISPR/Cas9-based gene editing of the NKG2A-encoding KLRC1 gene. Single-cell multi-omic analyses revealed a higher proportion of activated cells in CAR33-NK- and CAR33-KLRC1ko-NK pools, which were preserved following AML-cell contact. This activated state of the CAR33-KLRC1ko-NK cells has been translated into improved antileukemic activity in vitro and in vivo against AML cell lines and primary blasts. This dual modification of primary NK cells has the potential to bypass the suppressive effect not only of AML but also in a broad range of other cancer identities.

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Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory [scATAC in vitro]

Project description:Clonal expansion and epigenetic inheritance shape long-lasting NK cell memory [scATAC in vitro]

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Cytokine induced NK memory transcriptional profile characterization

Project description:By comparing CD94-CD56dim NK cell with or without primary stimulation treatment after 5 days, cytokine induced NK memory related molecules were identified.

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Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq]

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