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Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [Bulk RNA-seq]

ABSTRACT: Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [Bulk RNA-seq]

PROVIDER: PRJNA1051573 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27185821_1.fastq.gz	Fastqsanger.gz
	SRR27185821_2.fastq.gz	Fastqsanger.gz
	SRR27185822_1.fastq.gz	Fastqsanger.gz
	SRR27185822_2.fastq.gz	Fastqsanger.gz
	SRR27185823_1.fastq.gz	Fastqsanger.gz

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Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [Bulk RNA-seq]

Project description:Allogeneic natural killer (NK) cell therapies are a valuable treatment option for cancer, given their remarkable safety and favorable efficacy profile. Although the use of allogeneic donors allows for off-the-shelf and timely patient treatment, intrinsic interindividual differences put clinical efficacy at risk. The identification of donors with superior anti-tumor activity is essential to ensure the success of adoptive NK cell therapies. Here, we investigated the heterogeneity of 10 umbilical cord blood stem cell-derived NK cell batches. First, we evaluated the donors’ cytotoxic potential against tumor cell lines from solid and hematological cancer indications, to distinguish a group of superior, “excellent” killers (4/10), compared to “good” killers (6/10). Next, bulk and single-cell RNA-Sequencing, performed at different stages of NK differentiation, revealed distinct transcriptomic features of the two groups. Excellent donors showed an enrichment in cytotoxicity pathways and a depletion of myeloid traits, linked to the presence of a larger population of effector-like NK cells early on during differentiation. Consequently, we defined a multi-factorial gene expression signature able to predict the donors’ anti-tumor potential. Our study contributes to the identification of key traits of superior NK cell batches, supporting the development of efficacious NK therapeutics and the achievement of durable anti-tumor responses

2024-10-10 | GSE249991 | GEO

Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [scRNA-seq]

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Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity

Project description:Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity

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Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [scRNA-seq]

Project description:Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior anti-tumor activity [scRNA-seq]

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Microarray comparison of NK cell from healthy donors and day 14 post stem cell transplantation

Project description:NK cells were first isolated from PBMCs using EasySepâ¢ Human NK cell enrichment kit (STEMCELL biotechnology). The magnetically isolated NK cells were stained with anti-CD3 FITC, anti-CD56 Pe-Cy7 and LIVE/DEADÂ® red stain for a further enrichment, whereby the CD3 negative and CD56 positive live cells were sorted with MoFloâ¢ cell sorter (Beckman Coulter). The sorted NK cell populations were sent to AROS Applied Biotechnology A/S (Aarhus N, Denmark) to be analysed using GeneChipÂ® Human Transcriptome Array 2.0 (Affymetrix, USA). The transcription profile of NK cells from day 14 post stem cell transplantation was compared with those from healthy donors.

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Project description:NK cells are lymphocytes that provide a first defense against viral infections and cancer. They act (i) cytotoxic by killing virus-infected and tumorigenic cells and (ii) immune regulatory by releasing cytokines and chemokines. These innate immune cells are commonly further classified as CD56bright and CD56dim NK cells. Former studies confirmed immune regulatory CD56bright NK cells as progenitors of cytotoxic CD56dim NK cells. CD57 was previously described as T cell marker for senescence and terminal differentiation. Recent studies detected CD57+ and CD57- NK cells among the CD56dim NK cell population and suggested a fully mature developmental status for CD57+ NK cells. The recent NK cell maturation model includes CD34+ hematopoietic stem cells (HSC), which develop into CD56bright NK cells, later into CD56dimCD57- and finally into terminally maturated CD56dimCD57+ (1) (2) (3). The molecular mechanisms of human NK cell differentiation and maturation remain unknown to this date. We performed for the first time a proteomic analysis of these distinct developmental stages of human primary NK cells, isolated from overall 10 healthy human blood donors. CD56bright NK cells versusCD56dim and CD56dimCD57- versus CD56dimCD57+ NK cells were analyzed by using quantitative peptide sequencing, which revealed individual protein signatures (3400 proteins) of these different NK cell developmental stages. Notably, our data support the current NK cell differentiation model by highlighting both strong distinctions between CD56dim/bright NK cells and close relationships between CD57+/- NK cells on the proteomic level. Among the most prominent and conserved regulated proteins, we detected myosin IIa, Calvasculin and Calcyclin with very similar expression patterns. We investigated their sub-cellular localization and observed specific recruitment- and accumulation-events at the NK cell immunological synapse (NKIS) after NK activation.

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