Natural Killer Cell Diversity Research Articles

A Pan-Cancer Single-Cell Transcriptomic Atlas of Natural Killer (NK) Cells Reveals Intrinsic and Extrinsic Mediators of NK Cell Anti-Tumor Functions

Background: Natural killer (NK) cells are critical mediators of anti-tumor immunity, engaging in direct cytotoxic responses and promoting pro-inflammatory immune microenvironments. The molecular mechanisms underlying these functions, however, have yet to be fully elucidated. This is due in part to a lack of understanding of the phenotypic and functional diversity of NK cells across cancer types. Here, we present a single-cell transcriptomic atlas of >250,000 NK cells spanning 340 patients across 17 cancer types to advance our understanding of tumor-infiltrating NK cells. Methods: We re-analyzed publicly available single-cell RNA-sequencing (scRNA-seq) datasets of primary, therapy-naïve tumors, as well as matching peripheral blood samples and healthy donor blood samples. We employed systematic computational analyses to deconvolute the phenotypic and functional diversity of tumor-infiltrating NK cells and define key regulators of NK cell functions in both a cancer type-specific and pan-cancer manner. Feature expression module scoring was used to infer phenotypic and functional characteristics of NK cell clusters in each cancer type. Transcription factor regulon and cell-cell communication prediction algorithms were applied to understand the mechanistic drivers of NK cell populations within tumors. Results: Tumor-infiltrating NK cells display distinct patterns of phenotypic and functional features across cancer types. Nonetheless, we identify consensus NK cell populations across cancers that demonstrate the utility and performance of our gene module-based phenotypic and functional annotations. Interestingly, we observe the enrichment of adaptive-like and CD56 bright NK cell populations in tumors that exhibit features of tissue residency, including the upregulation of ITGA1, ITGAE, and CD69 alongside the downregulation of FCG3RA. Notably, these tissue-resident populations display enhanced chemokine and cytokine activity compared to their recruited counterparts, suggesting the significance of tissue-resident NK cell populations in immune recruitment to tumors. We find the phenotypic composition of intra-tumoral NK cells is vastly different than that of circulating NK cells which harbor predominantly CD56 dim populations, as well as a significant proportion of adaptive-like NK cells in several cancer types. Leveraging the paired nature of several tumor and peripheral blood samples, we performed temporal comparative analyses that revealed the robust expression of KLF2 and S1PR5 in circulation which is then lost in paired tumor tissues. While KLF2 and S1PR5 have been previously implicated in the homing and migration of immune cells, their roles in the trafficking of NK cells to tumors have yet to be defined. In modeling transitions from canonical to stressed NK cell states, we not only identify well-established NK cell checkpoints ( TIM-3, LAG3, and CISH) but also identify novel putative checkpoints yet to be investigated in NK cells, such as the AP-1 family of transcription factors. Additionally, we examine extrinsic factors contributing to intra-tumoral NK cell phenotypes, detecting significant crosstalk between NK cells and immunomodulatory macrophages and CD4+ T cells mediated by galectin-9 and TGFβ interactions. Conclusions: We define the phenotypic and functional pan-cancer landscape of NK cells and uncover both intrinsic and extrinsic factors influencing their anti-tumor functions. We envision our NK cell atlas will facilitate the development of strategies to enhance NK cell-based immunotherapies against cancer.

High dimensional analysis reveals distinct NK cell subsets but conserved response to stimulation in umbilical cord blood and adult peripheral blood.

Growing interest surrounds adoptive cellular therapies utilizing Natural Killer (NK) cells, which can be obtained from various sources, including umbilical cord blood (UCB) and adult peripheral blood (APB). Understanding NK cell receptor expression and diversity in such cellular sources will guide future therapeutic designs. We used a 20-color flow cytometry panel to compare unstimulated and cytokine-activated UCB and APB NK cells. Our analysis showed that UCB NK cells express slightly higher levels of the immune checkpoints PD-1, TIGIT, and CD96 compared to their APB counterparts. Unsupervised hierarchical clustering and dimensionality reduction analyses revealed enrichment in CD56neg as well as mature NKp46neg and CD56+ CD16+ NK cell populations in UCB whereas CD57+ terminally differentiated NK cells with variable expression of KIRs and CD16 were found in APB. These populations were conserved following stimulation with IL-12, IL-15, and IL-18. Cytokine stimulation was associated with the downregulation of TIGIT and CD16 on multiple NK cell subsets in UCB and APB. Among UCB CD16- NK cell populations, TIGIT+ NK cells produced more IFN-γ than their TIGIT- counterparts. Our data demonstrate higher immune checkpoint expression on UCB NK cells compared to APB. However, the expression of TIGIT immune checkpoint is not indicative of NK cell exhaustion.

Phenotypic diversity of human adipose tissue-resident NK cells in obesity.

Natural killer (NK) cells have emerged as key mediators of obesity-related adipose tissue inflammation. However, the phenotype of NK cell subsets residing in human adipose tissue are poorly defined, preventing a detailed understanding of their role in metabolic disorders. In this study, we applied multicolor flow cytometry to characterize CD56bright and CD56dim NK cells in blood and adipose tissue depots in individuals with obesity and identified surface proteins enriched on adipose tissue-resident CD56bright NK cells. Particularly, we found that adipose tissue harbored clusters of tissue-resident CD56bright NK cells signatured by the expression of CD26, CCR5 and CD63, possibly reflecting an adaptation to the microenvironment. Together, our findings provide broad insights into the identity of NK cells in blood and adipose tissue in relation to obesity.

Alzheimer's disease alters the transcriptomic profile of natural killer cells at single-cell resolution.

Alzheimer's disease (AD) is the most common dementia without an effective cure at least partially due to incomplete understanding of the disease. Inflammation has emerged as a central player in the onset and progression of AD. As innate lymphoid cells, natural killer (NK) cells orchestrate the initiation and evolution of inflammatory responses. Yet, the transcriptomic features of NK cells in AD remain poorly understood. We assessed the diversity of NK cells using web-based single-cell RNA sequencing data of blood NK cells from patients with AD and control subjects and flow cytometry. We identified a contraction of NK cell compartment in AD, accompanied by a reduction of cytotoxicity. Unbiased clustering revealed four subsets of NK cells in AD, i.e., CD56bright NK cells, CD56dim effector NK cells, adaptive NK cells, and a unique NK cell subset that is expanded and characterized by upregulation of CX3CR1, TBX21, MYOM2, DUSP1, and ZFP36L2, and negatively correlated with cognitive function in AD patients. Pseudo-temporal analysis revealed that this unique NK cell subset was at a late stage of NK cell development and enriched with transcription factors TBX21, NFATC2, and SMAD3. Together, our study identified a distinct NK cell subset and its potential involvement in AD.

The functional diversity of tissue-resident natural killer cells against infection.

For decades, studies of natural killer (NK) cells have focused on those found in peripheral blood (PBNK cells) as the prototype for NK cell biology. Only recently have researchers begun to explore the diversity of tissue-resident NK (tr-NK) cells. While tr-NK cells were initially identified from mice parabiosis and intravascular staining experiments, they can also be identified by tissue retention markers such as CD69, CD103 and others. More importantly, tr-NK cells have distinct functions compared to PBNK cells. Within the liver, there are diverse subsets of tr-NK cells expressing different combinations of tissue-retention markers and transcription factors, the clinical relevance of which are still unclear. Functionally, liver tr-NK are primed with immediate responsiveness to infection and equipped with regulatory mechanisms to prevent liver damage. When decidual NK (dNK) cells were first discovered, they were mainly characterized by their reduced cytotoxicity and functions related to placental development. Recent studies, however, revealed different mechanisms by which dNK cells prevent uterine infections. The lungs are one of the most highly exposed sites for infection due to their role in oxygen exchange. Upon influenza infection, lung tr-NK cells can degranulate and produce more inflammatory cytokines than PBNK cells. Less understood are gut tr-NK cells which were recently characterized in infants and adults for their functional differences. In this mini-review, we aim to provide a brief overview of the most recent discoveries on how several tr-NK cells are implicated in the immune response against infection.

Diversity of human NK cell developmental pathways defined by single-cell analyses.

Human natural killer (NK) and innate lymphoid cells (ILCs) include diverse specialized phenotypic and functional subsets that reflect their roles as innate immune effector cells present in tissue and circulation. In recent years, significant advances have been made in better defining their tissue resident phenotypes, developmental pathways, and phenotypic plasticity. Here we offer a brief review of new insights into human NK cell diversity specifically defined by next generation sequencing and single-cell transcriptomic studies and integrate these into our current models of human NK cell developmental trajectories and mature subsets. These studies highlight both a deeper understanding of innate lymphoid cell differentiation and homeostasis and underscore critical questions that remain outstanding in the field.

NK Cell Diversity Influences Outcomes after Cord Blood Transplantation

Natural killer (NK) cells are the first subset of lymphocytes to reconstitute, and likely play an important role in the graft-versus-leukemia response early after allogeneic hematopoietic stem cell transplantation. NK cells are highly diverse, and express an array of activating and inhibiting receptors, which delicately regulate their activation status.To provide a framework to better understand NK cell development and maturation after cord blood transplantation (CBT) and its implication on clinical outcomes, we designed a mass cytometry (also known as cytometry by time of flight) panel of 40 monoclonal antibodies recognizing lineage markers, NK cell receptors and transcription factors to interrogate the NK cell repertoire in prospectively collected peripheral blood (PB) samples from 60 CBT recipients. The resultant high-dimensional single cell data were analyzed by t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension reduction algorithm to generate expression profile graphs.With this mass cytometry platform, we first interrogated and compared the NK cell repertoire in CB (n=10) and adult peripheral blood (PB) (n=20) and used inverse Simpson index to measure the diversity of the NK cell populations. NK cells from CB donors had a significantly lower diversity (median 537, range 311-891) compared to NK cells from healthy adult PB donors (median 2858, range 1228-5630; p<0.0001). Since CMV infection has been shown to drive NK cell maturation, we next asked if CMV infection also alters NK cell diversity by comparing the diversity of the NK cell repertoire in CB (n=10), and in PB from adult healthy donors who were either CMV-seropositive (n=10), or CMV-seronegative (n=10). The diversity of the NK cell repertoire was significantly greater in CMV seropositive healthy individuals (median 4217, range 2672-5630) compared to CMV-seronegative healthy adults (median 2247 , range 2026-2468; P=0.0002) and cord blood donors (median 537, range 311-891; P<0.0001), pointing to an important role for CMV infection in driving NK diversity.Harnessing mass cytometry, we undertook an in-depth examination of the NK repertoire in prospectively collected PB samples from 60 CBT recipients. We first sought to determine if CMV infection early after CBT can drive NK cell maturation and accelerate the acquisition of a diverse repertoire. The median time to CMV reactivation for the cohort was 71 days. CMV reactivation in the first 100 days after CBT (n=25) was associated with significantly greater NK diversity (median 844, range 198-1196) when compared to patients without CMV reactivation (median 405, range 110-889; p=0.0003). Notably, CMV augmented NK diversity mainly in the KIR+ population (median 743, range 207-1500) compared to the KIR- population (median 361, range 92-1038; p=0.007); while in the absence of CMV reactivation, NK cell diversity in the KIR+ and KIR- populations remained similar (median 305, range 102-702 vs. median 332, range 54-830; p=0.98). These data indicate that CMV infection augments NK diversity after CBT, and that this effect is most pronounced within the KIR+ population.We next determined if NK cell diversity can influence outcomes by comparing the diversity of the NK cell repertoire in PB samples collected in the first 100 days after CBT from 15 patients who went on to relapse compared to 45 patients who remained in remission for 2 years. NK cell diversity was significantly higher (median 839, range 416-1069) in patients who remained in remission compared to those who progressed and relapsed (median 446, range 328-925; p=0.03). Moreover, the greatest difference in diversity in the two groups was noted within the KIR+ population (median 788, range 101-1500 for patients in remission vs median 320, range 177-857 for patients who relapsed; p=0.002).In summary, we have used multiparametric mass cytometry to examine expression of 40 NK markers, and to gain insights into the diversity of the NK cell repertoire after CBT. We have shown that CB NK cells have a limited NK cell diversity, which increases in breadth and subsets after transplant. Moreover, we observed that CMV infection reconfigures the NK cell compartment and drives the diversity of the NK cell repertoire, especially within the KIR+ population. These data may provide the basis to rationally design therapeutic strategies that can modulate NK diversity in the settings of infection and transplant. DisclosuresNo relevant conflicts of interest to declare.

CS1-Specific Chimeric Antigen Receptor Drives Cord Blood NK Cell Maturation and Expansion In Vivo

Chimeric antigen receptors (CAR) have been used extensively to redirect the specificity of T cells against leukemic cells, with remarkable clinical responses in patients with lymphoid malignancies. CAR-transduced natural killer (NK) cells might serve as an alternative to CAR T cells as they lack the potential to cause GVHD, and could be made available as an off-the-shelf allogeneic product for immediate clinical use. Moreover, unlike CAR-T cells, CAR NK cells retain their intrinsic capacity to recognize and target tumor cells through their native receptors, in theory making disease escape through downregulation of the CAR target antigen less likely. We have identified cord blood (CB) as a readily available source of allogeneic NK cells.Thus, in this study, we reprogrammed CB-NK cells to recognize multiple myeloma (MM) using a retroviral construct encoding a CAR against CS1, a coreceptor expressed on MM cells, IL-15 to enhance their in vivo proliferation and survival, and inducible caspase-9, a suicide gene that can be activated as needed. We consistently achieved a median CAR positivity of >90%, 14 days post transduction and viability of >95% with only limited CS1-mediated fratricide (since CS1 is also expressed on NK cells) during long-term ex vivo culture. CS1-CAR NK cells killed the CS1-expressing MM.1S cell line significantly better than ex vivo expanded non-transduced (NT) CB-NK cells at all effector:target ratios tested (p<0.001). We next tested the in vivo trafficking and antitumor activity of iC9/CAR.CS1/IL-15+ CB-NK cells in a xenograft mouse model of MM. Mice engrafted with MM1.S cells received saline (control) or 1 x107 ex vivo expanded CB-NK cells that were either unmodified or transduced with iC9/CAR.CS1/IL-15; iC9/CAR.CS1/IL15+ CB-NK cells controlled tumor expansion and prolonged survival of mice significantly better than NT CB-NK cells.This was associated withsignificantly higher frequencies of circulating NK cells in the CAR+ CB-NK cell treated mice (median=19%, range 13.6-31.1%) compared to the NT CB-NK group (median=1.26%, range 0.98-2.49%, p=0.0003). We next used mass cytometry (CyTOF) to interrogate the features that shape NK cell diversity, their maturation and their trafficking in vivo. The expression of CAR.CS1 on NK cells infiltrating tumor sites remained stable over time in vivo (median 86.7%, range 81-89.8% compared to the infused product). This was associated with significantly less tumor infiltration in liver (0.013% vs 33.8%), spleen (0.01% vs 23.4%) and BM (4.3% vs 79.8%) harvested on day 21 post-infusion, compared to mice treated with NT NK cells. Interestingly, the residual MM cells in the BM of iC9/CAR.CS1/IL-15 treated mice lost CS1 expression on their surface, suggesting that target antigen downregulation may also play a part in escape from CAR-mediated immune recognition in MM, as also described with CD19 CAR T cell therapy.Using a panel of 40 monoclonal antibodies, we profiled the global signature of NK cells harvested from organs of animals sacrificed on day 21 after infusion and compared them to CAR+ CB-NK cells prior to infusion. The diversity of iC9/CAR.CS1.IL-15-transduced CB-NK cells, measured using the inverse Simpson index, was similar to that of ex vivo expanded NT CB-NK cells (167 vs 114). Additionally, using t-SNE maps to visualize the high-dimensional data generated by CyTOF, we observed complete overlap of clusters for ex vivo expanded NT CB-NK cells and CS1-CAR-transduced CB-NK cells, indicating, that any potential CS1-related fratricide does not significantly impact on the repertoire of the CAR-transduced CB-NK cells (Figure 1).Interestingly, there was a profound and significant increase in the diversity of the infiltrating CS1-CAR CB-NK cells in the liver (830), spleen (843) and BM (965) on day 21 after infusion, suggesting in vivo maturation and expansion of NK subpopulations in response to the tumor. t-SNE analysis revealed a clear separation between iC9/CAR.CS1.IL-15 transduced CB-NK cells prior to infusion and tissue-infiltrating CAR+ CB-NK cells, indicating significant shifts in NK subpopulations, with an increase in diversity and maturation after adoptive transfer in vivo (Figure 1). The data from this analysis will have important implications for future studies as we seek to generate CAR+ CB-NK cells with enhanced antitumor potential. [Display omitted] DisclosuresNeelapu:Karus: Research Funding; Poseida Therapeutics, Inc: Research Funding; Bristol-Myers Squibb: Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Kite Pharma: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Cellectis Inc.: Research Funding; Merck: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Orlowski:BioTheryX: Consultancy, Membership on an entity's Board of Directors or advisory committees.

Insights Into Human Intrahepatic NK Cell Function From Single Cell RNA Sequencing Datasets.

Diverse populations of natural killer (NK) cells have been identified in circulating peripheral blood and a wide variety of different tissues and organs. These tissue-resident NK cell populations are phenotypically distinct from circulating NK cells, however, functional descriptions of their roles within tissues are lacking. Recent advances in single cell RNA sequencing (scRNA-seq) have enabled detailed transcriptional profiling of tissues at the level of single cells and provide the opportunity to explore NK cell diversity within tissues. This review explores potential novel functions of human liver-resident (lr)NK cells identified in human liver scRNA-seq studies. By comparing these datasets we identified up-regulated and down-regulated genes associated with lrNK cells clusters. These genes encode a number of activating and inhibiting receptors, as well as signal transduction molecules, which highlight potential unique pathways that lrNK cells utilize to respond to stimuli within the human liver. This unique receptor repertoire of lrNK cells may confer the ability to regulate a number of immune cell populations, such as circulating monocytes and T cells, while avoiding activation by liver hepatocytes and Kupffer cells. Validating the expression of these receptors on lrNK cells and the proposed cellular interactions within the human liver will expand our understanding of the liver-specific homeostatic roles of this tissue-resident immune cell population.

Host genetic control of natural killer cell diversity revealed in the Collaborative Cross

Natural killer (NK) cells are innate effectors armed with cytotoxic and cytokine-secreting capacities whose spontaneous antitumor activity is key to numerous immunotherapeutic strategies. However, current mouse models fail to mirror the extensive immune system variation that exists in the human population which may impact on NK cell-based therapies. We performed a comprehensive profiling of NK cells in the Collaborative Cross (CC), a collection of novel recombinant inbred mouse strains whose genetic diversity matches that of humans, thereby providing a unique and highly diverse small animal model for the study of immune variation. We demonstrate that NK cells from CC strains displayed a breadth of phenotypic and functional variation reminiscent of that reported for humans with regards to cell numbers, key marker expression, and functional capacities. We took advantage of the vast genetic diversity of the CC and identified nine genomic loci through quantitative trait locus mapping driving these phenotypic variations. SNP haplotype patterns and variant effect analyses identified candidate genes associated with lung NK cell numbers, frequencies of CD94+ NK cells, and expression levels of NKp46. Thus, we demonstrate that the CC represents an outstanding resource to study NK cell diversity and its regulation by host genetics.

Droplet-Based Cytotoxicity Assay: Implementation of Time-Efficient Screening of Antitumor Activity of Natural Killer Cells

Natural killer (NK) cells are key players of the innate immune system. Due to their rapid cytotoxicity against infectious pathogens, hematologic malignancies, and solid tumors, NK cells represent solid candidates for cell-based immunotherapy. Despite the progress made in recent years, the heterogeneity in their cytotoxic behavior represents a drawback. With the goal of screening the intrinsic diversity of NK cells, droplet-based microfluidic technology is exploited to develop a single-cell time-efficient cytotoxicity assay. Toward this end, NK-92 cells are coencapsulated with hematological tumor cell lines in water-in-oil droplets of different sizes and their cytotoxic activity is evaluated. The effect of droplet-based confinement on NK cytotoxicity is investigated by controlling the droplet volume. The successful optimization of the droplet size allows for time efficiency compared to cytotoxicity assays based on flow cytometry. Additionally, the ability of individual NK-92 cells to kill multiple target cells in series is explored, expanding the knowledge about the serial killing process dynamics. The developed droplet-based microfluidic assay does not require the labeling of NK cells and represents a step toward developing of a forthcoming process for the selection of NK cells with the highest cytotoxicity against specific targets.

NK Cell Memory to Cytomegalovirus: Implications for Vaccine Development.

Natural killer (NK) cells are innate lymphoid cells that recognize and eliminate virally-infected and cancerous cells. Members of the innate immune system are not usually considered to mediate immune memory, but over the past decade evidence has emerged that NK cells can do this in several contexts. Of these, the best understood and most widely accepted is the response to cytomegaloviruses, with strong evidence for memory to murine cytomegalovirus (MCMV) and several lines of evidence suggesting that the same is likely to be true of human cytomegalovirus (HCMV). The importance of NK cells in the context of HCMV infection is underscored by the armory of NK immune evasion genes encoded by HCMV aimed at subverting the NK cell immune response. As such, ongoing studies that have utilized HCMV to investigate NK cell diversity and function have proven instructive. Here, we discuss our current understanding of NK cell memory to viral infection with a focus on the response to cytomegaloviruses. We will then discuss the implications that this will have for the development of a vaccine against HCMV with particular emphasis on how a strategy that can harness the innate immune system and NK cells could be crucial for the development of a vaccine against this high-priority pathogen.

Tissue-Specific NK Cell Diversity in Solid Tumors

Abstract Cytotoxic innate lymphoid cells, conventionally known as natural killer (NK) cells, play major roles in cancer immunity largely due to their natural cytolytic and immune regulatory functions. However, due to the extensive heterogeneity and plasticity seen among NK cells, their functions have yet to be fully harnessed in immunotherapy. The objective of this study is to elucidate NK cell diversity maturation, recruitment and effector function profiling in solid tumor microenvironments. We hypothesize that NK cells from different tissue locations display genetic and functional profiles that can predict NK effectiveness in solid tumor microenvironments. Here, we show the biological diversity that exists among NK cells from different locations pre- and post-interaction with solid breast cancer tumors, including heterogeneity of NK cell specific cluster of differentiation markers and gene expression perspectives based on flow cytometry, qPCR, RNA, and bioinformatics analyses. Understanding NK cells in the tumor microenvironment could help answer critical NK cell research questions and lead to advancements in cancer immunotherapy applications, ultimately helping to mitigate the cancer resources-results discrepancy.

Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing

Human natural killer (NK) cells in peripheral blood perform many functions, and classification of specific subsets has been a longstanding goal. We report single-cell RNA sequencing of NK cells, comparing gene expression in unstimulated and interleukin (IL)-2-activated cells from healthy cytomegalovirus (CMV)-negative donors. Three NK cell subsets resembled well-described populations; CD56brightCD16-, CD56dimCD16+CD57-, and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells subdivided to include a population with higher chemokine mRNA and increased frequency of killer-cell immunoglobulin-like receptor expression. Three novel human blood NK cell populations were identified: a population of type I interferon-responding NK cells that were CD56neg; a population exhibiting a cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2; and finally, a small population, with low ribosomal expression, downregulation of oxidative phosphorylation, and high levels of immediate early response genes indicative of cellular activation. Analysis of CMV+ donors established that CMV altered the proportion of NK cells in each subset, especially an increase in adaptive NK cells, as well as gene regulation within each subset. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analyzing NK cell responses in health and disease.

Subordinate Effect of -21M HLA-B Dimorphism on NK Cell Repertoire Diversity and Function in HIV-1 Infected Individuals of African Origin.

Natural Killer (NK) cells play an important role in antiviral defense and their potent effector function identifies them as key candidates for immunotherapeutic interventions in chronic viral infections. Their remarkable functional agility is achieved by virtue of a wide array of germline-encoded inhibitory and activating receptors ensuring a self-tolerant and tunable repertoire. NK cell diversity is generated by a combination of factors including genetic determinants and infections/environmental factors, which together shape the NK cell pool and functional potential. Recently a genetic polymorphism at position -21 of HLA-B, which influences the supply of HLA-E binding peptides and availability of HLA-E for recognition by the inhibitory NK cell receptor NKG2A, was shown to have a marked influence on NK cell functionality in healthy human cytomegalovirus (HCMV) seronegative Caucasian individuals. In this study, -21 methionine (M)-expressing alleles supplying HLA-E binding peptides were largely poor ligands for inhibitory killer immunoglobulin-like receptors (KIRs), and a bias to NKG2A-mediated education of functionally-potent NK cells was observed. Here, we investigated the effect of this polymorphism on the phenotype and functional capacity of peripheral blood NK cells in a cohort of 36 African individuals with human immunodeficiency virus type 1 (HIV-1)/HCMV co-infection. A similarly profound influence of dimorphism at position -21 of HLA-B on NK cells was not evident in these subjects. They predominantly expressed African specific HLA-B and -C alleles that contribute a distinct supply of NKG2A and KIR ligands, and these genetic differences were compounded by the marked effect of HIV-1/HCMV co-infection on NK cell differentiation. Together, these factors resulted in a lack of correlation of the HLA-B -21 polymorphism with surface abundance of HLA-E and loss of the NK cell functional advantage in subjects with -21M HLA-B alleles. Instead, our data suggest that during HIV/HCMV co-infection exposure of NK cells to an environment that displays altered HLA-E ligands drives adaptive NKG2C+ NK cell expansions influencing effector responses. Increased efforts to understand how NK cells are functionally calibrated to self-HLA during chronic viral infections will pave the way to developing targeted therapeutic interventions to overcome the current barriers to enhancing immune-based antiviral control.

Seq-ing out the Killers of Mice and Men

The diversity of natural killer cells between mouse and human is poorly understood. In this issue of Immunity, Crinier etal. (2018) utilize single-cell RNA-seq to profile splenic and blood NK cells from both organisms, uncovering both tissue- and species-specific transcriptomic signatures.

Irreversible impact of chronic hepatitis C virus infection on human natural killer cell diversity.

Diversity is crucial for the immune system to efficiently combat infections. Natural killer (NK) cells are innate cytotoxic lymphocytes that contribute to the control of viral infections. NK cells were for long thought to be a homogeneous population of cells. However, recent work has instead revealed NK cells to represent a highly diverse population of immune cells where a vast number of subpopulations with distinct characteristics exist across tissues. However, the degree to which a chronic viral infection affects NK cell diversity remains elusive. Hepatitis C virus (HCV) is effective in establishing chronic infection in humans. During the last years, new direct-acting antiviral drugs (DAA) have revolutionized treatment of chronic hepatitis C, enabling rapid cure in the majority of patients. This allows us to study the influence of a chronic viral infection and its subsequent elimination on the NK cell compartment with a focus on NK cell diversity. In our recent study (Nat Commun, 9:2275), we show that chronic HCV infection irreversibly impacts human NK cell repertoire diversity.

Chronic hepatitis C virus infection irreversibly impacts human natural killer cell repertoire diversity

Diversity is a central requirement for the immune system’s capacity to adequately clear a variety of different infections. As such, natural killer (NK) cells represent a highly diverse population of innate lymphocytes important in the early response against viruses. Yet, the extent to which a chronic pathogen affects NK cell diversity is largely unknown. Here we study NK cell functional diversification in chronic hepatitis C virus (HCV) infection. High-dimensional flow cytometer assays combined with stochastic neighbor embedding analysis reveal that chronic HCV infection induces functional imprinting on human NK cells that is largely irreversible and persists long after successful interventional clearance of the virus. Furthermore, HCV infection increases inter-individual, but decreases intra-individual, NK cell diversity. Taken together, our results provide insights into how the history of infections affects human NK cell diversity.

Maturation of cord blood natural killer (NK) cells differs among neonates

Abstract The source, timing of colonization, and stability of the neonatal microbiome is largely unknown. We and other groups recently demonstrated that infant colonization may begin in utero, challenging the notion that neonates are born sterile. However, neonates are particularly vulnerable to viral infection partially due to dampened responses from NK cells and delayed maturation of adaptive immunity. Given the degree of variability in neonatal vulnerability to infection, we hypothesized that intrauterine exposure to microbes enables a greater diversity of NK cells in the neonates, relative to the adult, to allow for immune tolerance. Here, we performed multi-parametric flow cytometry analyses to dissect the normal range and expression of human NK cell developmental markers from umbilical cord (UC) blood (n=37). NK cells were identified as CD45+ CD3− CD56+ using FlowJo X and Cytobank. UC blood had a lower frequency of mature NK cells than adult peripheral blood. Furthermore, examination of NK cell maturation via spanning analysis of density events (SPADE) highlighted inter-individual diversity of neonatal NK cell subsets. Diversity of NK cells subsets between neonates and adults was significantly different with higher diversity in neonates (Simpson’s Diversity Index, p = 0.008). Our findings suggest diversity in stages of NK cell development between individual neonates that may reflect early immune exposure. Given ours and others recent work demonstrating that the intrauterine environment is not sterile, we speculate that microbial exposures during gestation may be a driving difference in the diversification NK cell populations in human infants and hence enable immune tolerance at the risk of neonatal viral vulnerability.

284: Maturation of cord blood natural killer (NK) cells differs among neonates

The source, timing of colonization, and stability of the neonatal microbiome is largely unknown, and it remains unclear how microbes influence early immunity. We and others have recently shown that infant colonization may begin in utero, challenging the notion that neonates are born sterile. However, some neonates are particularly vulnerable to viral infection, which is thought to be due to dampened responses from NK cells and delayed maturation of adaptive immunity. Given the degree of variability in neonatal vulnerability to infection, we hypothesized that intrauterine exposure to microbes in the more common non-sterile environment actually enables a greater diversity of NK cells in the neonates relative to the adult to allow for immune tolerance. Here, we performed the largest multi-parametric flow cytometry analyses to dissect the normal range and expression of human NK cell developmental markers from umbilical cord (UC) blood. UC blood was collected at delivery in a large number of neonates (n=35). Whole blood was stained with NK cell maturation markers and data was acquired by flow cytometry. Data was analyzed using FlowJo X and Cytobank. Spanning analysis density of events (SPADE) analysis was applied to identify NK cell developmental subsets by individual. Diversity between neonates and adults was calculated using Simpson’s Diversity Index. NK cells were identified in UC blood as CD3−CD45+CD56+. UC blood had a lower frequency of mature NK cells than adult peripheral blood (Fig. A) Furthermore, examination of NK cell maturation via SPADE analysis identified highlighted inter-individual diversity of neonatal NK cell subsets (Fig. B). Diversity of NK cells subsets between neonates and adults was significantly different with higher diversity in neonates (Fig. C, p = 0.008). Our findings suggest diversity in stages of NK cell development between individual neonates that may reflect early immune exposure and harken viral susceptibility. Given ours and others recent work demonstrates that the intrauterine environment is not sterile, we speculate that microbial exposures during gestation may be a driving difference in the diversification NK cell populations in human infants and hence enable immune tolerance at the risk of neonatal viral vulnerability.