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Updated: Jun 11, 2025
Generation of Natural Killer Cells from Human Expanded Potential Stem Cells
Published on: January 13, 2023
Bulk and single-cell transcriptomics identify gene signatures of stem cell-derived NK cell donors with superior
Amanda A van Vliet1,2,3,4,5, Mirjam G C N van den Hout6, Daniëlle Steenmans1
1Glycostem Therapeutics, Kloosterstraat 9, 5349 AB Oss, the Netherlands.
Abstract:
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 with "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' cytotoxic 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.
Insights
Identifying superior donors is key for effective allogeneic natural killer (NK) cell cancer therapy. This study defines a gene expression signature to predict NK cell cytotoxic potential for improved treatment outcomes.
Area of Science:
- Immunology
- Cancer Biology
- Cell Therapy
Background:
- Allogeneic natural killer (NK) cell therapies offer a promising, off-the-shelf treatment for cancer.
- Interindividual variability in donor NK cell efficacy poses a challenge to treatment success.
- Identifying donors with superior anti-tumor activity is crucial for optimizing adoptive NK cell therapies.
Purpose of the Study:
- To investigate the heterogeneity of umbilical cord blood stem cell-derived NK cell batches.
- To distinguish between "excellent" and "good" NK cell donors based on cytotoxic potential.
- To identify transcriptomic features and develop a predictive signature for superior NK cell batches.
Main Methods:
- Evaluated cytotoxic potential of 10 NK cell batches against solid and hematological cancer cell lines.
- Performed bulk and single-cell RNA sequencing at various NK differentiation stages.
- Defined a multi-factorial gene expression signature to predict donor cytotoxic potential.
Main Results:
- Identified 4/10 "excellent" killer donors and 6/10 "good" killer donors.
- Observed distinct transcriptomic profiles between "excellent" and "good" donors.
- Excellent donors exhibited enriched cytotoxicity pathways, depleted myeloid traits, and an early-emerging effector-like NK cell population.
Conclusions:
- Established a gene expression signature to predict NK cell donor cytotoxic potential.
- Highlighted key traits associated with superior NK cell batches for cancer therapy.
- Supports the development of more efficacious NK cell therapeutics for durable anti-tumor responses.
