Heterogeneity Of Natural Killer Cells Research Articles

Highlight of 2023: From fundamental studies to clinical trials, the importance of NK cells against cancer.

In this article for the Highlights of 2023 Series, we discuss how various factors affect the ability of natural killer (NK) cells to fight tumors. For instance, tumor cells can hinder NK cell function by reducing surface protrusions or increasing HLA-E expression via platelets. Lower UTX protein levels in male NK cells also decrease their cytotoxicity compared with females. Fortunately, recent advancements in therapeutic approaches have emerged, including the development of a comprehensive atlas of NK cell heterogeneity within the tumor microenvironment, as well as a trispecific engager molecule that has shown promise in enhancing the anti-tumor functions of NK cells.

A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response

We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use Tcell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. Tcell InteractPrint was predictive of response in both trials versus PD-L1 (AUC= 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.

Single-cell profiling reveals the heterogeneity of NK cells during anti-PD-1 therapy in non-small-cell lung cancer

BackgroundThe efficacy of immune checkpoint inhibitors remains limited in non-small cell lung cancer (NSCLC). Natural killer (NK) cells serve as the key element of innate immunity and play an important role in anti-tumor immunity, the impact of NK cells on efficacy of anti-PD-1 therapy in NSCLC is worth exploring. MethodsWe analyzed single-cell transcriptome data derived from biopsies of NSCLC patients receiving anti-PD-1 treatment. Immune cell subtypes were identified and further cell–cell communication were analyzed and verified. ResultsWe observed totally 6 distinct NK cells clusters in NSCLC infiltrating immune cells. It’s worth noting that enrichment of immature NK cells was found in responsive group. A series of marker genes of immature NK cells were associated with anti-PD-1 response and related to immune regulation processes such as antigen processing, Th1, Th17 cells activation. Moreover, effector CD8+ T cells were significantly enriched in responsive group and showed similar trajectories with immature NK cells. Cell-cell communication analysis showed that immature NK cells showed strong interactions with Th17 cells and effector CD8+ T cells. Furthermore, when validating the expression of immature NK cells marker genes, we found that CXCR4 was associated with enriched infiltration of CD8+ T cells. ConclusionsIn conclusion, immature NK cells may facilitate the efficacy of anti-PD-1 therapy by interacting with Th1 cells, Th17 cells and enhancing infiltration of effector CD8+ T cells. Our data suggested that NK cells could be a promising target to improve the prognosis of NSCLC patients.

Brief IL-12, IL-15, IL-18 activation drives the acquisition of two distinct memory-like NK cell states

Abstract IL-12/15/18 activation induces natural killer (NK) cell differentiation into cytokine-induced memory-like (ML) NK cells with enhanced IFNγ and killing of tumor targets that is antigen independent, rendering them distinct from conventional (cNK) and CMV-induced adaptive NK cells. In leukemia patients, ML NK cells have an excellent safety profile and 47% CR rate (PMID: 32826231). Despite their clinical promise, little is known about the biology underlying ML NK cells. Based on individual variability of human ML NK cell function, we hypothesized that ML NK cells manifest molecular heterogeneity. To this end, we applied Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to profile RNA and protein expression on the single-cell level, and evaluated NK cell function. Overnight IL-12/15/18 stimulation induced broad activation with distinct transcriptional programs evident in CD56 brightcompared to CD56 dimNK cells. In contrast, following in vitrodifferentiation for 7 days, IL-12/15/18 activated NK cells acquired a unique transcriptional and protein signature, and manifest one of two ML NK cell states (ML-1, ML-2), or remained similar to cNK cells. ML-1 was marked by increased activating receptor expression (NKp46, NKp30, NKp44) while ML-2 had increased expression of inhibitory receptors, CD25, HLA-DR, MKI67, and IFNG. In functional assays, ML-2 cells produced more IFNγ following cytokine stimulation than ML-1 cells. Further, ML-1 and ML-2 had divergent transcription factor profiles suggesting distinct mechanisms of regulation. Collectively, our findings reveal molecular and functional heterogeneity of ML NK cells, and investigations into ML subsets in patients receiving ML NK cell therapy are ongoing. AAI Intersect Fellowship for Computational Scientists & Immunologists (JAF, TAF, AAP), T32GM139799 (JAF), P50CA171963 (TAF, MMB-E), R01CA205239 (TAF), P30CA91842 (TAF)

Etiology of end-stage liver cirrhosis impacts hepatic natural killer cell heterogenicity.

The natural killer (NK) cell population is a critical component of the innate immune compartment of the liver, and its functions are deeply affected by the surrounding environment. In the late stage of fibrosis, NK cells become dysfunctional, but the influence of disease etiology on NK cell behavior during cirrhosis remains unclear. Using single-cell RNA sequencing (scRNA-seq), we characterized the hepatic NK cells from end-stage cirrhotic livers from subjects with non-alcoholic steatohepatitis (NASH), chronic hepatitis C infection (HCV) and primary sclerosing cholangitis (PSC). Here, we show that although NK cells shared similar dysfunctions, the disease etiology impacts hepatic NK cell heterogeneity. Therapeutical strategies targeting NK cells for the prevention or treatment of fibrosis should consider liver disease etiology in their design.

The mechanobiology of NK cells- 'Forcing NK to Sense' target cells.

Natural killer (NK) cells are innate immune lymphocytes that recognize and kill cancer and infected cells, which makes them unique 'off-the-shelf' candidates for a new generation of immunotherapies. Biomechanical forces in homeostasis and pathophysiology accrue additional immune regulation for NK immune responses. Indeed, cellular and tissue biomechanics impact NK receptor clustering, cytoskeleton remodeling, NK transmigration through endothelial cells, nuclear mechanics, and even NK-dendritic cell interaction, offering a plethora of unexplored yet important dynamic regulation for NK immunotherapy. Such events are made more complex by the heterogeneity of human NK cells. A significant question remains on whether and how biochemical and biomechanical cues collaborate for NK cell mechanotransduction, a process whereby mechanical force is sensed, transduced, and translated to downstream mechanical and biochemical signalling. Herein, we review recent advances in understanding how NK cells perceive and mechanotransduce biophysical cues. We focus on how the cellular cytoskeleton crosstalk regulates NK cell function while bearing in mind the heterogeneity of NK cells, the direct and indirect mechanical cues for NK anti-tumor activity, and finally, engineering advances that are of translational relevance to NK cell biology at the systems level.

Tissue-specific transcriptional profiles and heterogeneity of natural killer cells and group 1 innate lymphoid cells

Natural killer (NK) cells and type 1 innate lymphoid cells (ILC1s) are populations of non-T, non-B lymphocytes in peripheral tissues. Although NK and ILC1 subsets have been described, their identification and characteristics remain unclear. We performed single-cell RNA sequencing and CITE-seq to explore NK and ILC1 heterogeneity between tissues. We observed that although NK1 and NK2 subsets are conserved in spleen and liver, ILC1s are heterogeneous across tissues. We identified sets of genes expressed by related subsets or characterizing unique ILC1 populations in each organ. The syndecan-4 appeared as a marker discriminating murine ILC1 from NK cells across organs. Finally, we revealed that the expressions of EOMES, GZMA, IRF8, JAK1, NKG7, PLEK, PRF1, and ZEB2 define NK cells and that IL7R, LTB, and RGS1 differentiate ILC1s from NK cells in mice and humans. Our data constitute an important resource to improve our understanding of NK-ILC1 origin, phenotype, and biology.

Heterogeneity of liver NK cells

<p indent="0mm">Natural killer (NK) cells have attracted much attention since their discovery in the 1970s; however, earlier studies mainly focused on circulating NK cells. In the past decade, the heterogeneity of NK cells in different tissues has begun to attract increasing attention. As an organ containing abundant and heterogeneous NK cell populations, the liver provides a good window for studying them. It is now commonly accepted that bulk liver NK cells comprise circulating conventional NK cells and liver-resident NK cells. This review summarized and discussed the developmental origin, differentiation, transcriptional regulation, and immune functions of liver-resident NK cells and conventional NK cells, providing new perspectives for studying liver regional immunity.

Natural Killer Cells in Multiple Sclerosis: Entering the Stage.

Studies investigating the immunopathology of multiple sclerosis (MS) have largely focused on adaptive T and B lymphocytes. However, in recent years there has been an increased interest in the contribution of innate immune cells, amongst which the natural killer (NK) cells. Apart from their canonical role of controlling viral infections, cell stress and malignancies, NK cells are increasingly being recognized for their modulating effect on the adaptive immune system, both in health and autoimmune disease. From different lines of research there is now evidence that NK cells contribute to MS immunopathology. In this review, we provide an overview of studies that have investigated the role of NK cells in the pathogenesis of MS by use of the experimental autoimmune encephalomyelitis (EAE) animal model, MS genetics or through ex vivo and in vitro work into the immunology of MS patients. With the advent of modern hypothesis-free technologies such as single-cell transcriptomics, we are exposing an unexpected NK cell heterogeneity, increasingly blurring the boundaries between adaptive and innate immunity. We conclude that unravelling this heterogeneity, as well as the mechanistic link between innate and adaptive immune cell functions will lay the foundation for the use of NK cells as prognostic tools and therapeutic targets in MS and a myriad of other currently uncurable autoimmune disorders.

Tissue-Specific Imprinting and Heterogeneity of Natural Killer Cells and Group 1 Innate Lymphoid Cells

Tissue-Specific Imprinting and Heterogeneity of Natural Killer Cells and Group 1 Innate Lymphoid Cells

Single-Cell Transcriptomic Analysis Reveals Loss of Activated Bone Marrow NK Cells in Multiple Myeloma Patients Which Associates with Disease Progression in Mice

IntroductionMultiple Myeloma (MM) disease progression and therapy response are the net result of tumor cell-intrinsic features and tumor cell-extrinsic cues from the bone marrow (BM) microenvironment. Natural killer (NK) cells are mediators of the cytotoxic immune response against MM and are important effector cells in antibody-based immune therapies, especially anti-CD38 monoclonal antibodies such as Daratumumab. Classically, NK cells are divided into a cytotoxic CD56 dim subset, important for antibody-dependent cellular cytotoxicity, and a cytokine-producing CD56 bright subset releasing inflammatory mediators such as IFNγ, TNFα and GM-CSF. However, accumulating evidence suggests greater heterogeneity in the NK cell compartment and modulation of these NK cell subsets could impact disease progression and response to NK cell-driven immunotherapies. Here, we combined the 5TGM1 murine model of MM with single-cell RNA sequencing of bone marrow (BM) NK cells of newly diagnosed MM patients to map NK cell heterogeneity and to investigate their role in MM progression.ResultsTo gain insight in NK cell heterogeneity in MM disease we performed single-cell RNA sequencing on immune cells of viably frozen BM aspirates from 19 newly diagnosed MM patients and 5 non-cancer control patients. NK cells were identified in silico by transcription of KLRF1, KLRD1, GNLY and NKG7 resulting in a single-cell transcriptomic dataset of 30,373 NK cells from MM patients and 8,865 NK cells from control patients. Conventional CD56 bright and CD56 dim NK-cells were identified by increased transcription of GZMK or GZMB, respectively. The GZMK +CD56 bright NK cells contained clusters of naïve and activated NK cells. The GZMB+CD56 dim NK cells consisted of 5 subclusters. To identify MM-induced alterations in NK cell subsets, we compared GZMK +CD56 bright vs GZMB+CD56 dim cluster composition and distribution between controls and MM patients. Control BM was dominated by GZMB-transcribing cytotoxic CD56 dim NK cells, resulting in a low ratio of cytokine-producing GZMK +CD56 bright vs cytotoxic GZMB+CD56 dim NK cells. In contrast, MM bone marrow was characterized by heterogeneity of this ratio with a subset of patients presenting with complete reversal of this ratio . In this subset of patients, the altered composition was due to a loss of cytotoxic GZMB +CD56 dim NK cells, and more specifically a loss of NK cells with a transcriptome suggesting recent activation.To better examine the significance of cytotoxic NK cells in MM disease course we utilized the well-established 5TGM1 mouse model. C57Bl/6 and KaLwRij mice both received 10 6 5TGM1-GFP cells intravenously. Three weeks after tumor injection all KaLwRij mice (18/18) developed MM, defined by >5% tumor cells in BM (“unrestrained tumor”) and serum M-protein >2mg/ml. Interestingly, while 39% (7/18) of C57Bl/6 mice had no tumor, 44% (8/18) had low but detectable levels of MM cells (0.1-5% of BM cells, “restrained tumor”) and 17% (3/18) presented with an unrestrained MM with BM tumor load similar to that seen in KaLwRij mice. With time the percentage of mice with unrestrained tumor increased (5/12, 42%) at the expense of restrained tumor (2/12, 16%). We hypothesized that C57Bl/6 mice with low tumor load could represent a model of immune-mediated tumor control. Detailed analysis of the NK cell compartment revealed an expansion of activated mature (CD69 + CD11b +CD27 +) NK cells in C57Bl/6 mice with restrained BM MM (p=0.0031). In contrast, high BM tumor burden in both genotypes was associated with a sharp decline in absolute numbers of activated NK cells.Conclusion:Through a combination of single-cell transcriptomic analyses of the BM immune microenvironment in MM patients and experimental mouse models we found a loss of activated NK cells in a subset of patients and mice. Our data suggests that loss of these activated NK cells is associated with MM progression in vivo. A subset of MM patients presented with a loss of activated cytotoxic GZMB +CD56 dim NK cells in the BM, suggestive of reduced cytotoxic anti-tumor responses. Meanwhile, in vivo, high disease burden only occurred in mice with an absence of activated NK cells. Current analyses are focused on differences in human disease progression and efficacy of Daratumumab-based therapies in patients with various NK cell phenotypes. DisclosuresBroijl: Janssen, Amgen, Sanofi, Celgene/BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees. Sonneveld: Janssen: Consultancy, Honoraria, Research Funding; Karyopharm: Consultancy, Honoraria, Research Funding; Celgene/BMS: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria, Research Funding; SkylineDx: Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Research Funding.

EZH2 identifies the precursors of human natural killer cells with trained immunity.

Objective:Trained immunity of natural killer (NK) cells has shown great potential in the treatment of cancers by eliciting enhanced effector responses to restimulation by cytokines or cancer cells for long time periods after preactivation. However, the human NK cells responsible for the generation and maintenance of trained immunity are largely unknown. We hypothesized that heterogeneous human NK cells would respond differentially to stimulation with a combination of IL-12, IL-15, and IL-18, and that an NK cell subset might exist that is mainly responsible for the induction of trained immunity. On the basis of our hypothesis, we aimed to identify the subset from which cytokine-trained human NK cells originate and to explore possible regulatory targets for drug intervention.Methods:Flow cytometry assays were performed to analyze the functions of cytokine-trained NK cells and examine cell division and protein expression in NK cell subsets. Single-cell RNA sequencing (scRNA-seq) plus TotalSeq™ technology was used to track the heterogeneity of NK cells during the induction of trained immunity.Results:Traditional developmental markers for peripheral NK cells were unable to identify the precursors of human NK cells with trained immunity. Therefore, we used scRNA-seq plus TotalSeq™ technology to track the heterogeneity of NK cells during the induction of trained immunity and identified a unique cluster of CD57−NKG2A+EZH2+IFNG+MKI67+IL12R+IL15R+IL18R+ NK cells. Enrichment and pseudotime trajectory analyses suggested that this cluster of NK cells contained the precursor of trained NK cells. We then used flow cytometry to further investigate the role of EZH2 in trained NK precursors and found that CD57−NKG2A+EZH2+ NK cells had faster cell cycles and an enhanced trained phenotype, and EZH2 inhibition significantly impaired the induction of trained immunity in NK cells. These results suggested that EZH2 is a unique epigenetic marker of precursors of human NK cells with trained immunity.Conclusions:Our work revealed human NK heterogeneity in the induction of trained immunity, identified the precursor subset for trained NK cells, and demonstrated the critical role of EZH2 in the induction of trained immunity in human NK cells.

An automated real-time microfluidic platform to probe single NK cell heterogeneity and cytotoxicity on-chip

Cytotoxicity is a vital effector mechanism used by immune cells to combat pathogens and cancer cells. While conventional cytotoxicity assays rely on averaged end-point measures, crucial insights on the dynamics and heterogeneity of effector and target cell interactions cannot be extracted, emphasizing the need for dynamic single-cell analysis. Here, we present a fully automated droplet-based microfluidic platform that allowed the real-time monitoring of effector-target cell interactions and killing, allowing the screening of over 60,000 droplets identifying 2000 individual cellular interactions monitored over 10 h. During the course of incubation, we observed that the dynamics of cytotoxicity within the Natural Killer (NK) cell population varies significantly over the time. Around 20% of the total NK cells in droplets showed positive cytotoxicity against paired K562 cells, most of which was exhibited within first 4 h of cellular interaction. Using our single cell analysis platform, we demonstrated that the population of NK cells is composed of individual cells with different strength in their effector functions, a behavior masked in conventional studies. Moreover, the versatility of our platform will allow the dynamic and resolved study of interactions between immune cell types and the finding and characterization of functional sub-populations, opening novel ways towards both fundamental and translational research.

NK cell and ILC heterogeneity in colorectal cancer. New perspectives from high dimensional data

Innate lymphoid cells (ILCs) and tissue-resident natural killer (NK) cells ensure immunity at environmental interfaces and help maintain barrier integrity of the intestinal tract. This wide range of innate lymphocytes is able to provide fast and potent inflammatory responses that, when deregulated, have been associated with pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC). While the presence of tumor-infiltrating NK cells is generally associated with a favorable outcome in CRC patients, emerging evidence reveals distinct roles for ILCs in regulating CRC pathogenesis and progression. Advances in next generation sequencing technology, and in particular of single-cell RNA-seq approaches, along with multidimensional flow cytometry analysis, have helped to deconvolute the complexity and heterogeneity of the ILC system both in homeostatic and pathological contexts. In this review, we discuss the protective and detrimental roles of NK cells and ILCs in the pathogenesis of CRC, focusing on the phenotypic and transcriptional modifications these cells undergo during CRC development and progression.

NK cells ride the uterine cycle

Natural Killer Cells Tissue-resident natural killer (NK) cells in the uterus promote successful pregnancies by regulating the depth of placental trophoblast invasion. Endometrial tissue is naturally subject to constant remodeling in response to hormonal fluctuations during the menstrual cycle, but how the changing uterine microenvironment influences the heterogeneity of uterine NK (uNK) cells is poorly understood. Strunz et al. used proteomic and transcriptomic techniques to profile human uNK cells recovered from different stages of the menstrual cycle and during pregnancy. This analysis identified sequentially expressed uNK cell surface markers that define a recurring cycle of differentiation in response to progesterone-regulated release of stromal interleukin-15. These findings pave the way for further studies on how uNK cell functions are modulated by the dynamic endometrial microenvironment. Sci. Immunol. 6 , eabb7800 (2021).

Droplet‐Based Combinatorial Assay for Cell Cytotoxicity and Cytokine Release Evaluation

AbstractBalancing the maximal efficacy of interferon gamma (IFN‐ɣ)‐based therapies with its side effects is a great challenge for future cytokine treatments. To achieve this, the development of single‐cell technologies that study IFN‐ɣ release in correlation with antitumor activity would represent a huge step forward. To this end, droplet‐based microfluidics is employed to quantitatively investigate IFN‐ɣ secretion from single natural killer (NK) cells in correlation with their cytotoxic activity against a specific target. The method relies on co‐encapsulation of NK‐92 cells, target cancer cells, polystyrene beads conjugated with specific IFN‐ɣ capture antibodies, and fluorescently labeled detection antibodies inside water‐in‐oil compartments. The secreted cytokines are captured and detected by localized fluorescence at the periphery of the beads. NK‐92's cytotoxicity is evaluated simultaneously by means of a fluorescent DNA intercalating agent, which penetrates the membranes of dead target cells. To deepen the understanding of the role of the cytokine in antitumor immunomodulation, the impact of different doses of human recombinant IFN‐ɣ on the cytolytic activity of NK‐92 cells shows a trend that the higher the dose the lower the cytolytic activity of NK cells. The developed method represents a simple quantitative approach to unravel the complex heterogeneity of NK cells toward IFN‐ɣ secretion and cytolytic activity.

Tissue-Resident NK Cells: Development, Maturation, and Clinical Relevance.

Natural killer (NK) cells belong to type 1 innate lymphoid cells (ILC1) and are essential in killing infected or transformed cells. NK cells mediate their effector functions using non-clonotypic germ-line-encoded activation receptors. The utilization of non-polymorphic and conserved activating receptors promoted the conceptual dogma that NK cells are homogeneous with limited but focused immune functions. However, emerging studies reveal that NK cells are highly heterogeneous with divergent immune functions. A distinct combination of several activation and inhibitory receptors form a diverse array of NK cell subsets in both humans and mice. Importantly, one of the central factors that determine NK cell heterogeneity and their divergent functions is their tissue residency. Decades of studies provided strong support that NK cells develop in the bone marrow. However, evolving evidence supports the notion that NK cells also develop and differentiate in tissues. Here, we summarize the molecular basis, phenotypic signatures, and functions of tissue-resident NK cells and compare them with conventional NK cells.

CD49a+CD49b+ NK cells induced by viral infection reflect an activated state of conventional NK cells.

Natural killer (NK) cells are important innate effectors that play a pivotal role in the defense against tumors and infections and participate in regulating adaptive immunity. Recent studies have revealed phenotypic and functional heterogeneity of NK cells. Here, using murine models of acute and chronic lymphocytic choriomeningitis virus infection, we observed that a CD49a+ CD49b+ NK cell subset emerged in the liver and other tissues, and underwent vigorous expansion following viral infection, before progressively decreasing in cell number. These viral infection-induced CD49a+CD49b+ NK cells displayed an activated and mature phenotype. Moreover, compared with liver-resident NK cells and conventional NK (cNK) cells, CD49a+CD49b+ NK cells showed increased functional competence, as evidenced by higher amounts of IFN-γ production and stronger cytotoxic capabilities during viral infection. Generation of these CD49a+CD49b+ NK cells was shown to be independent of the T-bet transcription factor. Adoptive transfer experiments revealed that cNK cells could convert into CD49a+CD49b+ NK cells following viral infection. Collectively, these results suggest that viral infection-induced CD49a+CD49b+ NK cells represent a transiently activated state of cNK cells.

Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome

Natural killer (NK) cells are critical to both innate and adaptive immunity. However, the development and heterogeneity of human NK cells are yet to be fully defined. Using single-cell RNA-sequencing technology, here we identify distinct NK populations in human bone marrow and blood, including one population expressing higher levels of immediate early genes indicative of a homeostatic activation. Functionally matured NK cells with high expression of CX3CR1, HAVCR2 (TIM-3), and ZEB2 represents terminally differentiated status with the unique transcriptional profile. Transcriptomic and pseudotime analyses identify a transitional population between CD56bright and CD56dim NK cells. Finally, a donor with GATA2T354M mutation exhibits reduced percentage of CD56bright NK cells with altered transcriptome and elevated cell death. These data expand our understanding of the heterogeneity and development of human NK cells.

A collagen-based microwell migration assay to study NK-target cell interactions

Natural killer (NK) cell cytotoxicity in tissue is dependent on the ability of NK cells to migrate through the extracellular matrix (ECM) microenvironment. Traditional imaging studies of NK cell migration and cytotoxicity have utilized 2D surfaces, which do not properly reproduce the structural and mechanical cues that shape the migratory response of NK cells in vivo. Here, we have combined a microwell assay that allows long-term imaging and tracking of small, well-defined populations of NK cells with an interstitial ECM-like matrix. The assay allows for long-term imaging of NK–target cell interactions within a confined 3D volume. We found marked differences in motility between individual cells with a small fraction of the cells moving slowly and being confined to a small volume within the matrix, while other cells moved more freely. A majority of NK cells also exhibited transient variation in their motility, alternating between periods of migration arrest and movement. The assay could be used as a complement to in vivo imaging to study human NK cell heterogeneity in migration and cytotoxicity.