NK cells are innate immune cells known for their cytolytic activities toward tumors and infections. They are capable of expressing diverse killer Ig-like receptors (KIRs), and KIRs are implicated in susceptibility to Crohn’s disease (CD), a chronic intestinal inflammatory disease. However, the cellular mechanism of this genetic contribution is unknown. In this study, we show that the “licensing” of NK cells, determined by the presence of KIR2DL3 and homozygous HLA-C1 in host genome, results in their cytokine reprogramming, which permits them to promote CD4+ T cell activation and Th17 differentiation ex vivo. Microfluidic analysis of thousands of NK single cells and bulk secretions established that licensed NK cells are more polarized to proinflammatory cytokine production than unlicensed NK cells, including production of IFN-γ, TNF-α, CCL-5, and MIP-1β. Cytokines produced by licensed NK augmented CD4+ T cell proliferation and IL-17A/IL-22 production. Ab blocking indicated a primary role for IFN-γ, TNF-α, and IL-6 in the augmented T cell–proliferative response. In conclusion, NK licensing mediated by KIR2DL2/3 and HLA-C1 elicits a novel NK cytokine program that activates and induces proinflammatory CD4+ T cells, thereby providing a potential biologic mechanism for KIR-associated susceptibility to CD and other chronic inflammatory diseases.

Natural killer cells are components of the innate immune system primarily known for cytolytic targeting of tumor cells and virally infected cells. Despite their apparent role in the development of many chronic inflammatory diseases (16), their functional role in pathogenesis is poorly understood. Recent human genome-wide association analysis has uncovered gene expression networks of NK cells implicated in inflammatory bowel disease (IBD) pathogenesis (7). However, due to the complex roles and functional proficiencies of NK cell subpopulations, the biologic mechanisms of their involvement in chronic inflammatory diseases, and the ones pertinent to IBD, remain uncertain (14, 8, 9).

Killer Ig-like receptor (KIR) genes are predominantly expressed by NK cells, and are one element of the receptor repertoire controlling NK cell activation, proliferation, and effector functions that mediate surveillance and host defense for microbial infection and malignancy (10, 11). The genetic combination of KIRs with their respective HLA class I ligands is associated with multiple autoimmune disorders, infectious diseases, and cancers (5, 6). However, the functional mechanisms accounting for these disease associations, particularly for the inhibitory class of KIRs, are poorly understood. The KIR gene family is composed of 14 functional genes (seven activating, six inhibitory, one bifunctional) and 2 pseudogenes (12). The KIR locus exhibits haplotypes with extensive variations in number and types of KIR genes. Among the inhibitory KIRs, KIR2DL1 recognizes HLA-C2 allotypes, KIR2DL2 and KIR2DL3 recognize HLA-C1 allotypes, KIR3DL1 recognizes HLA-Bw4 (5, 12). Accordingly, functional pairings of cognate HLA and KIR genes in an individual haplotype is quite heterogeneous, which confounds studies of their biologic function.

This study was prompted by the elevated genetic susceptibility for Crohn’s disease (CD) in patients bearing the inhibitory KIR2DL2/3 with its cognate ligand HLA-C1 (1315). This association was puzzling, because NK–target interaction via inhibitory KIR ligation suppresses NK effector function (2, 16). One potential explanation is the licensing effects of inhibitory KIRs during NK differentiation. Licensing is a maturational process, induced by signaling of select inhibitory KIR genes with their cognate HLA ligands during NK differentiation that confers expanded functional competence of NK cells. Because the presence of relevant pairs of inhibitory KIR and cognate HLA genes are stochastic, healthy individuals genetically vary in the presence or abundance of licensed NK cells. Also, although the known NK cell functions affected by licensing include augmented target cell killing and IFN-γ production (16, 17), there has been little study of NK licensing on other aspects of NK cell function: regulation of inflammation and adaptive immunity or the scope of licensing-related cytokine and chemokine production (18).

Mechanistic studies of human NK cell licensing are challenging due to the complex genetic composition of KIR-HLA combinations (12), and the conflicting roles inhibitory and activating KIRs play in licensing. Therefore, we focused on individuals homozygous for the KIR A haplotype (termed AA haplotype), a common genotype (∼30% worldwide) which contains inhibitory KIRs for three key HLA class I ligands (HLA-C1, HLA-C2, and HLA-Bw4) but only one single activating KIR (12, 19). Different inhibitory KIR-HLA class I ligand pairs confer various levels of strength for NK licensing (Supplemental Table I) (20). The most potent pair is KIR2DL3/HLA-C1; the second strongest pair is KIR3DL1/HLA-Bw4, whereas KIR2DL1/HLA-C2 has minimal licensing effect. Because AA haplotype individuals have KIR2DL3 and KIR2DL1, we consider individuals with homozygous HLA-C1 (abbreviated as HLA-C1C1) strongly licensed individuals and individuals with HLA-C1/HLA-C2 or homozygous HLA-C2 (abbreviated as HLA-C2+) weakly licensed or unlicensed individuals.

Therefore, we aimed to investigate the potential of NK licensing in the KIR associated CD susceptibility. In this study, we show that NK cells from genetically licensed healthy subjects and CD patients efficiently augment antigenic CD4+ T cell proliferation, and this augmentation is mediated by soluble molecules secreted by licensed NK cells. Licensed NK cell supernatant also dramatically promotes Th17 cells, a signature CD4+ Th subset in CD. Multiplexed cytokine study of CD cohort demonstrated that genetically licensed and unlicensed NK cells exhibit consistent and distinct cytokine profiles, with licensed NK cells distinguished by high-output, proinflammatory, poly-cytokine expression. Selected cytokines among this output account for the capacity of licensed NK cells to efficiently augment antigenic CD4+ T cell proliferation and Th17 polarization.

Clinical samples were collected according to protocols approved by the institutional review committee of Cedars-Sinai Medical Center (CSMC) and of University of California, Los Angeles (UCLA). CD patients, previously genotyped for HLA and KIR (13), were randomly chosen, consented and called back by CSMC. Of the 1306 patients, 455 are AA haplotype, 28 consented for callback blood donation, and all 20 subjects who returned for collection were included for study. Healthy donors were recruited at UCLA Clinical and Translational Research Laboratory and genotyped by the UCLA Immunogenetics Center.

PBMCs were isolated by Ficoll–Paque (GE Healthcare, Chalfont St. Giles, U.K.) density gradient centrifugation. Human NK cells were purified either from whole blood using the RosetteSep Human NK cell enrichment Cocktail or from PBMC using the Human NK cell negative selection kit (StemCell Technologies, Vancouver, BC, Canada). Human regulatory T cell–depleted T cells were purified from PBMC using a Human T cell enrichment kit and CD25-positive selection kit; CD4+ T cells were purified from PBMC using a Human T cell enrichment kit and CD4-positive selection kit (StemCell Technologies). The purity of isolated NK cells and T cells were confirmed to be above 90%.

Before coculture, round bottom 96-well plates were coated with anti-CD3/CD28 Ab (R&D Systems, Minneapolis, MN) in PBS at 1.5 μg ml−1 at room temperature for 2 h or at 0.5 μg ml−1 at 4°C overnight. T cells were stained with 0.2 μM CFSE (Invitrogen, Carlsbad, CA) and cocultured with NK cells for 3 d in 96-well plates at 1 × 106 cells ml−1 in presence of 2 ng ml−1 (26 IU) IL-2 with complete RPMI 1640 medium, containing 10% FBS, 100 IU ml−1 penicillin 100 μg mL−1 streptomycin, 10 mM HEPES buffer, 2 mM glutamine (Cellgro, Manassas, VA), and 5 × 10−5 M 2-ME (Sigma-Aldrich, St. Louis, MO). Blocking Abs for OX40 ligand and 2B4 (CD 252 and CD244; R&D Systems) were added to the coculture at concentration of 10 μg ml−1. Neutralizing Abs, for IL-6, IFN-γ, TNF-α, and isotype control mouse IgG1κ (eBioscience, San Diego, CA), and their combinations were added to the coculture at 1.25 μg ml−1. The recombinant cytokines IL-6, IFN-γ, and TNF-α (R&D Systems) was each added to a final concentration of 20 ng ml−1, comparable to the concentration measured for these cytokines in NK cell 3-d culture media analyzed by multiplex ELISA chip. For Transwell assay, 24-well plates were used; NK cells were placed on the filter side of a 1.0-μm pore-sized Transwell (BD Falcon, San Jose, CA), and CFSE-stained T cells were placed on the plate side of the Transwell.

Before culturing, round bottom 96-well plates were coated with 1 μg ml−1 anti-CD3 (R&D Systems) in PBS for 2 h at room temperature, and washed with 5% human AB Serum RPMI 1640 medium (Lonza, Rockland, ME). Total CD4+ T cells were purified and stimulated with 0.2 μg ml−1 soluble anti-CD28, primed with different percentages of NK supernatants, and in the presence or absence of various cytokine combinations. At day 6 or 7, CD4+ T cells were resuspended, washed once with media, and expanded with 2 ng ml−1 (26 IU) IL-2 plus the same conditions provided for priming. At day 14, the cells were stimulated with PMA/ionomycin and brefeldin A for 5 h. Cells were then surface stained with anti-CD3, intracellularly stained with anti–IFN-γ, anti–IL-22, and anti–IL-17A, followed by flow using LSRII (BD Biosciences, San Jose, CA).

CD NK cells were isolated using the Human NK cell negative selection kit (StemCell Technologies). NK cells were cultured for 3 d in round-bottom 96-well plate at 1 × 106 cells ml−1 in 2 ng ml−1 (26 IU) IL-2 with complete RPMI 1640 medium. Then media samples were collected, stored at −80°C. Before analysis, samples were thawed, concentrated four times, and assayed as one batch. The initial protein panel was chosen to incorporate immune function markers, consisting primarily of cytokines and chemokines that could be secreted by NK cells. The final NK secretion Ab panel was chosen to incorporate nonredundant secretions detectable at NK 3-d culture.

Frozen aliquots of PBMC were thawed and recovered overnight. Bulk NK cells were purified using the Human NK cell enrichment kit; CD3CD56dimKIR2DL3+KIR3DL1KIR2DL1 and CD3CD56dimKIR2DL3 NK subsets sorted by FACS. All cells were prepared on ice and immediately analyzed by a single-cell microchip. Briefly, the microchip proteomics platform is based on isolating individual or a small number of cells into several thousand ∼600 pl volume microchambers, with each chamber equipped with a miniaturized Ab array. These chips permitted the simultaneous measurement of 19 protein markers in each microchamber. After loading onto the single-cell barcode chip (SCBC), the cells were stimulated with 5 ng ml−1 PMA and 500 ng ml−1 ionomycin for 12 h at 37°C, and the microchip was imaged to count cell numbers within each microchambers. After cells were washed off, the fluorescence readouts were generated by an ELISA immunoassay and were quantified using a GenePix 4400A array scanner and custom-built software algorithms.

The following Abs and cell tracer were used staining for flow analysis: FITC-conjugated anti-CD158b (BD Biosciences), anti-IFN-γ (eBioscience, San Diego, CA); CFSE; PE-conjugated anti–IFN-γ (BD Biosciences), anti–TNF-α, anti–IL-22, anti-granzyme B (eBioscience), anti–GM-CSF (R&D Systems); PerCP-conjugated anti-CD3 (BD Biosciences); allophycocyanin-conjugated anti-CD158a (Miltenyi Biotec, Bergisch Gladbach, Germany), anti-CD4 (BD Biosciences), anti-IL-17A (eBioscience); strepavidin-PerCP; PE-Cy7–conjugated anti-CD56, anti-CD14 (BD Biosciences), Vioblue-conjugated anti-3DL1 (Miltenyi Biotec, Bergisch Gladbach, Germany), eFluor 650NC-conjugated anti-CD3 (eBioscience); anti-mouse IgG κ/Negative Control Compensation Particles. The use of Ab for staining was performed per manufacturer’s instructions with proper titrations. Abs used for cytokine assays are IL-2, IL-6, IL-10, IL-15, IL-13, CCL-4 (MIP-1β), CCL-5, CXCL-10, CCL-2, CXCL-8, IFN-γ, TNF-α, TNF-β, granzyme B, TGF-β1 (R&D Systems, Minneapolis, MN), IL-4, IL-12, GM-CSF, and perforin (eBioscience).

Phenotypic analysis of PBMC was performed using flow cytometry after staining of cells with fluorescence dye–conjugated Abs. Labeled cells were analyzed with a FACSCalibur flow cytometer using CellQuest software, or LSR II (BD Biosciences) using FACSDiva software (BD Biosciences) at UCLA Flow Cytometry Core, and data analysis was performed using FlowJo (Tree Star, Ashland, OR). Cells were sorted for CD3-CD56dimKIR2DL3+KIR3DL1KIR2DL1 and CD3CD56dim KIR2DL3, using Aria I equipped with FACSDiva software (BD Biosciences).

Most data analyses involved comparison of continuous variables, so the Student two-tailed unpaired t test was used; p < 0.05 were regarded as significant. All cytokine data were normalized before biostatistical analysis. GraphPad Prism (San Diego, CA) was used for statistical analysis and graphing. To uncover and visualize patient groups based on these parameters, we used principal component analysis (PCA) and hierarchical clustering, box-plot and scatter-plot analysis were performed in R package using custom-written codes. Microchip data from this study is available from our laboratory Web site (http://www.its.caltech.edu/∼heathgrp/).

Proinflammatory CD4+ Th cells are the main effectors in induction and perpetuation of intestinal inflammation (21, 22). As a major cellular component of innate immunity, NK cells demonstrably cross-talk with the adaptive immunity arm (3, 19, 2325). Because NK cells can stimulate or inhibit T cell activation via multiple mechanisms (2629), we first asked whether strongly and weakly licensed NK cells from CD patients differentially modulated T cell proliferation in vitro. We isolated blood NK cells and autologous T cells from CD patients (Table I), and cocultured them in the presence of immobilized anti-CD3/CD28 and IL-2 at 2 ng⋅ml−1 (26 IU). At day 3, CD4+ T cell proliferation was measured via CFSE dilution (Fig. 1A). CD4+ T cell proliferation was augmented linearly with the number of licensed NK cells present (R2 = 0.996; Fig. 1B). Using linearity (R2 > 0.85) as a quality control criterion, 12 patient assays were selected for genetic correlation analysis. At an NK:T ratio of 1:1, NK cells from HLA-C1C1 patients were significantly more potent than those from HLA-C2+ patients, and NK cells from HLA-Bw4/Bw4 patients were significantly more potent than those from HLA-Bw6+ individuals within the HLA-C2+ subset. Thus, three distinct levels of NK function were observed: HLA-C1C1 Bw6+ > HLA-Bw4/Bw4 > Bw6/+ HLA-C2+ (Fig. 1C), and this order conformed to KIR licensing strength (Supplemental Table I) (20).

Table I.
CD patient demographics
UCLA_IDHLA-BwHLA-CAge (y)GenderRaceAge of Diagnosis (y)Current Medication
CDKIR0804 Bw6 C1 63 Caucasian 19 None 
CDKIR0805-88 Bw4, Bw6 C1 55 Caucasian 18 Methotrexate, darifenacin, ciprofloxacin 
CDKIR0816 Bw4, Bw6 C1 50 Caucasian 26 Acetaminophen 
CDKIR0822 Bw4, Bw6 C1 60 Caucasian 28 Adalimumab, clonazepam mesalamine, pravastatin, zolpidem, alprazolam 
CDKIR0831 Bw6 C1 60 Caucasian 49 Glatiramer acetate, atorvastatin, bupropion, escitalopram, nitrofurantoin 
CDKIR0919 Bw6 C1 49 Caucasian 12 Mesalamine, rifaximin, hydrochlorothiazide, alprazolam, acetaminophen, and hydrocodone 
CDKIR0921 Bw4 C1 50 Caucasian 21 Methadone, fentanyl citrate, nexium 
CDKIR1130 Bw6 C1 40 Caucasian 25 Escitalopram, lorazepam 
CDKIR1207 Bw4 C1 44 Caucasian 30 6-Mercaptopurine, methotrexate, mesalamine 
CDKIR012512-49 Bw4, Bw6 C1 55 Caucasian 33 6-Mercaptopurine, infliximab, citalopram 
CDKIR0805-01 Bw6 C1, C2 48 Caucasian 26 Colesevelam, diphenoxylate and atropine, doxorubicin, cyclophosphamide, aprepitant, ondansetron, prochlorperazine 
CDKIR0811 Bw4, Bw6 C1, C2 62 Caucasian 25 Infliximab 
CDKIR0902 Bw4 C1, C2 41 Caucasian 33 Loestrin 4Fe, infliximab, propranolol, zolpidem 
CDKIR0914 Bw4 C1, C2 63 Caucasian 31 Adalimumab, diphenoxylate and atropine, colestipol, simvastatin, levothyroxine, montelukast, belladonna alkaloids and phenobarbital, acetaminophen and hydrocodone, escitalopram, ibandronate, fioricet 
CDKIR021712 Bw4, Bw6 C1, C2 40 Caucasian 22 Mesalamine, infliximab 
CDKIR022412 Bw6 C1, C2 47 Caucasian Lisinopril, fluoxetine, bupropion, prednisone 
CDKIR0805-04 Bw4, Bw6 C2 31 Caucasian 22 6-Mercaptopurine 
CDKIR0809 Bw4, Bw6 C2 46 Caucasian 30 Adalimumab, lisdexamfetamine, duloxetine, cyanocobalamin (b12) 
CDKIR1014 Bw4 C2 42 Caucasian 17 6-Mercaptopurine, dicyclomine, zolpidem, alprazolam, amlodipine besylate, metoprolol, prednisone, dexlansoprazole, ondansetron, adalimumab 
CDKIR012512-50 Bw4, Bw6 C2 43 Caucasian 33 Acetaminophen, cyclosporine, adalimumab, losartan potassium, cefuroxime 
UCLA_IDHLA-BwHLA-CAge (y)GenderRaceAge of Diagnosis (y)Current Medication
CDKIR0804 Bw6 C1 63 Caucasian 19 None 
CDKIR0805-88 Bw4, Bw6 C1 55 Caucasian 18 Methotrexate, darifenacin, ciprofloxacin 
CDKIR0816 Bw4, Bw6 C1 50 Caucasian 26 Acetaminophen 
CDKIR0822 Bw4, Bw6 C1 60 Caucasian 28 Adalimumab, clonazepam mesalamine, pravastatin, zolpidem, alprazolam 
CDKIR0831 Bw6 C1 60 Caucasian 49 Glatiramer acetate, atorvastatin, bupropion, escitalopram, nitrofurantoin 
CDKIR0919 Bw6 C1 49 Caucasian 12 Mesalamine, rifaximin, hydrochlorothiazide, alprazolam, acetaminophen, and hydrocodone 
CDKIR0921 Bw4 C1 50 Caucasian 21 Methadone, fentanyl citrate, nexium 
CDKIR1130 Bw6 C1 40 Caucasian 25 Escitalopram, lorazepam 
CDKIR1207 Bw4 C1 44 Caucasian 30 6-Mercaptopurine, methotrexate, mesalamine 
CDKIR012512-49 Bw4, Bw6 C1 55 Caucasian 33 6-Mercaptopurine, infliximab, citalopram 
CDKIR0805-01 Bw6 C1, C2 48 Caucasian 26 Colesevelam, diphenoxylate and atropine, doxorubicin, cyclophosphamide, aprepitant, ondansetron, prochlorperazine 
CDKIR0811 Bw4, Bw6 C1, C2 62 Caucasian 25 Infliximab 
CDKIR0902 Bw4 C1, C2 41 Caucasian 33 Loestrin 4Fe, infliximab, propranolol, zolpidem 
CDKIR0914 Bw4 C1, C2 63 Caucasian 31 Adalimumab, diphenoxylate and atropine, colestipol, simvastatin, levothyroxine, montelukast, belladonna alkaloids and phenobarbital, acetaminophen and hydrocodone, escitalopram, ibandronate, fioricet 
CDKIR021712 Bw4, Bw6 C1, C2 40 Caucasian 22 Mesalamine, infliximab 
CDKIR022412 Bw6 C1, C2 47 Caucasian Lisinopril, fluoxetine, bupropion, prednisone 
CDKIR0805-04 Bw4, Bw6 C2 31 Caucasian 22 6-Mercaptopurine 
CDKIR0809 Bw4, Bw6 C2 46 Caucasian 30 Adalimumab, lisdexamfetamine, duloxetine, cyanocobalamin (b12) 
CDKIR1014 Bw4 C2 42 Caucasian 17 6-Mercaptopurine, dicyclomine, zolpidem, alprazolam, amlodipine besylate, metoprolol, prednisone, dexlansoprazole, ondansetron, adalimumab 
CDKIR012512-50 Bw4, Bw6 C2 43 Caucasian 33 Acetaminophen, cyclosporine, adalimumab, losartan potassium, cefuroxime 
FIGURE 1.

NK cells from genetically licensed CD patients strongly augment autologous CD4+ T cell proliferation. NK cells and autologous T cells were isolated from AA haplotype CD patient peripheral blood, stimulated with anti-CD3 and anti-CD28, and cocultured in 2 ng ml−1 (26 IU) IL-2 for 3 d. (A) Histograms of CD4+ T cell CFSE dilution after coculturing with NK cells at the NK/T ratios as indicated, for a representative C1C1 CD patient (gated on CD4+CFSE+ cells). The number within each graph indicates the percentage of cells proliferated. (B) Correlation between NK/T ratio and change in CD4+ T cell division number in log scale, calculated as mean CFSE intensity at coculture/mean CFSE intensity of T cell alone. (C) Comparison of change in CD4+ T cells division number at NK/T = 1:1, among C1C1Bw6/+, Bw4/Bw4, and C2+Bw6/+ AA haplotype patients (n = 4, Student t test, two-tailed. **p < 0.005, ***p < 0.0005). (D) Histograms of CD4+ T cell CFSE dilution in the absence of (left two) or in the presence (right two panels) of the indicated blocking Abs at 10 μg ml−1 (gated on CD4+CFSE+ cells). (E) Histograms of CD4+ T cell CFSE dilution at the indicated NK/T ratio without physical separation of NK cells and T cells (left two panels) or with separation by 1.0-μm-pore size Transwells (right panel) (gated on CD4+CFSE+ cells). The numbers in each histogram indicate the percentage of proliferating cells.

FIGURE 1.

NK cells from genetically licensed CD patients strongly augment autologous CD4+ T cell proliferation. NK cells and autologous T cells were isolated from AA haplotype CD patient peripheral blood, stimulated with anti-CD3 and anti-CD28, and cocultured in 2 ng ml−1 (26 IU) IL-2 for 3 d. (A) Histograms of CD4+ T cell CFSE dilution after coculturing with NK cells at the NK/T ratios as indicated, for a representative C1C1 CD patient (gated on CD4+CFSE+ cells). The number within each graph indicates the percentage of cells proliferated. (B) Correlation between NK/T ratio and change in CD4+ T cell division number in log scale, calculated as mean CFSE intensity at coculture/mean CFSE intensity of T cell alone. (C) Comparison of change in CD4+ T cells division number at NK/T = 1:1, among C1C1Bw6/+, Bw4/Bw4, and C2+Bw6/+ AA haplotype patients (n = 4, Student t test, two-tailed. **p < 0.005, ***p < 0.0005). (D) Histograms of CD4+ T cell CFSE dilution in the absence of (left two) or in the presence (right two panels) of the indicated blocking Abs at 10 μg ml−1 (gated on CD4+CFSE+ cells). (E) Histograms of CD4+ T cell CFSE dilution at the indicated NK/T ratio without physical separation of NK cells and T cells (left two panels) or with separation by 1.0-μm-pore size Transwells (right panel) (gated on CD4+CFSE+ cells). The numbers in each histogram indicate the percentage of proliferating cells.

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To investigate the nature of interaction between NK and CD4+ T cells, we neutralized the surface costimulatory molecules 2B4 and OX40 ligand, expressed by NK cells to promote CD4+ T cell activation (2729). Surprisingly, augmentation was fully preserved when these surface molecules were blocked (Fig. 1D). To assess whether this interaction was contact-dependent at all, NK cells were separated from T cells using 1-μm pore Transwells, only allowing soluble mediators to communicate between the sides. Separating NK and CD4+ T cells did not affect CD4+ proliferation at all (Fig. 1E), suggesting that NK augmentation of CD4+ T cell proliferation was mainly mediated by soluble molecules secreted by licensed NK cells.

Multiple cytokines and chemokines are produced by NK cells (18), but little is known about the scope of cytokine reprogramming by KIR-mediated NK licensing. Therefore, we cultured NK cells for 3 d under the same condition used for NK-T cell coculture experiments, and quantitated the level of a panel of cytokines in the NK supernatant using a multiplex ELISA chip, which can simultaneously analyze up to 19 cytokines (30, 31). When supernatants of NK cells from HLA-C1C1 (strongly licensed) and HLA-C2+ (weakly licensed) CD patients were compared, NK cells from HLA-C1C1 patients were significantly more robust producers of nine cytokines (Fig. 2A). This was specific to NK cells, as cytokine production by T cells was indistinguishable between HLA-C1C1 and HLA-C2+ patients (data not shown). The core differences resided in CCL-5 and MIP-1β (chemokines important for neutrophil and T cell recruitment); and, IFN-γ, TNF-α, IL-6, and IL-4 (proinflammatory cytokines known to play a role in CD) (Fig. 2A). In contrast, both types of NK cells produced negligible IL-12, IL-15, or IL-10 (Fig. 2A), because their levels were at or below the background detection threshold. Hierarchical clustering (Fig. 2B) showed that HLA-C1C1 and HLA-C2+ patients were completely separated, demonstrating their distinct secretion capacities. To assess native NK cell activation state (CD69 expression), we compared six subjects (three HLA-C1C1 and three HLA-C2+). At the time of isolation, the frequency of CD69+ cells was significantly elevated in HLA-C1C1 NK cells compared with HLA-C2+ NK cells (data not shown, p = 0.018); CD69 expression was in most cultures stable after 24 h in low-dose IL-2. This observation suggested a potential positive correlation between CD69 expression and licensing-induced NK cell cytokine capacity.

FIGURE 2.

NK cells from HLA-C1C1 patients have distinct cytokine secretion patterns compared with those from HLA-C2+ patients in bulk culture. (A) Univariate comparison of cytokine production level of bulk culture NK cells from HLA-C1C1 CD patients with (licensing, solid dot) and HLA-C2+ patients (unlicensed, open square) genotypes. The vertical axis shows the fluorescence intensity. (n = 4–5, p values are calculated using two-tailed Student t test, adjusted for multiple comparison by false discovery rate, *p < 0.05, **p < 0.005, ***p < 0.0005). The dash line indicates the detection threshold. Secretion profiles were measured by multiplex ELISA. (B) Hierarchical clustering of the bulk cytokine production profile of NK cells from HLA-C1C1 (red) and HLA-C2+ (blue) CD patients. Each row represents one protein indicated on the right, and each column represents one patient. (n = 4–5).

FIGURE 2.

NK cells from HLA-C1C1 patients have distinct cytokine secretion patterns compared with those from HLA-C2+ patients in bulk culture. (A) Univariate comparison of cytokine production level of bulk culture NK cells from HLA-C1C1 CD patients with (licensing, solid dot) and HLA-C2+ patients (unlicensed, open square) genotypes. The vertical axis shows the fluorescence intensity. (n = 4–5, p values are calculated using two-tailed Student t test, adjusted for multiple comparison by false discovery rate, *p < 0.05, **p < 0.005, ***p < 0.0005). The dash line indicates the detection threshold. Secretion profiles were measured by multiplex ELISA. (B) Hierarchical clustering of the bulk cytokine production profile of NK cells from HLA-C1C1 (red) and HLA-C2+ (blue) CD patients. Each row represents one protein indicated on the right, and each column represents one patient. (n = 4–5).

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To investigate whether NK cells from AA haplotype licensed healthy donors have similar levels of functionality as licensed CD patients, we assessed their effects in CD4+ T cell coculture. Using the same coculture assays described earlier, we observed that CD4+ T cell proliferation increased linearly with the number of licensed NK cells present in the coculture (R2 = 0.949; Fig. 3A, 3B). At an NK:T ratio of 1:1, the effect on CD4+ T cells by NK cells from the 2 HLA-C1C1 healthy subjects was comparable that that of NK cells from HLA-C1C1 patients (Figs. 3C, and 1C).

FIGURE 3.

NK cells from HLA-C1C1 healthy subjects have comparable CD4+ T cell–augmenting capacity as HLA-C1C1 CD patients. (A) Histograms of CD4+ T cell CFSE dilution after coculturing with NK cells at the NK/T ratios as indicated, for a representative HLA-C1C1 healthy subject (gated on CD4+CFSE+ cells). The number within each graph indicates the percentage of cells proliferated. (B) Correlation between NK/T ratio and change in CD4+ T cell division number in log scale, calculated as mean CFSE intensity at coculture/mean CFSE intensity of T cell alone. (C) Change in CD4+ T cells division number at NK/T = 1:1 from two HLA-C1C1 healthy subjects.

FIGURE 3.

NK cells from HLA-C1C1 healthy subjects have comparable CD4+ T cell–augmenting capacity as HLA-C1C1 CD patients. (A) Histograms of CD4+ T cell CFSE dilution after coculturing with NK cells at the NK/T ratios as indicated, for a representative HLA-C1C1 healthy subject (gated on CD4+CFSE+ cells). The number within each graph indicates the percentage of cells proliferated. (B) Correlation between NK/T ratio and change in CD4+ T cell division number in log scale, calculated as mean CFSE intensity at coculture/mean CFSE intensity of T cell alone. (C) Change in CD4+ T cells division number at NK/T = 1:1 from two HLA-C1C1 healthy subjects.

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We speculated whether this secretion difference reflected a homogeneous functional change in the NK cell population, or instead a mosaic of cellular heterogeneity. Therefore, we assessed cytokine secretion profiles of individual NK cells at the single cell level using SCBCs (30), a high-throughput microfluidics platform. With SCBCs, single cells or a small number of cells are separated into thousands of microchambers on a chip, where the production of 19 cytokines is simultaneously and independently measured during a 12-h period. This technology has been extensively validated, and its utility in studying immune cell response has been demonstrated, as well as compared with standard flow assays (30).

We compared single NK cell cytokine secretion between two HLA-C1C1 and two HLA-C2+ CD patients, NK cells from HLA-C1C1 patients exhibited a higher output of multiple cytokines, including TNF-α, MIP-1β, GM-CSF, IFN-γ, IL-2, IL-6, and CXCL-10 (Fig. 4A, 4B, Supplemental Fig. 1). PCA of the single-cell data showed that NK cells with from HLA-C1C1 patients contained a subset that produced effector proteins (CCL-5, TNF-α, IFN-γ, MIP-1β, and IL-6), which in contrast was barely detected in NK cells from HLA-C2+ patients (Fig. 4C). When the composition of cells producing one, two, three, four, five, and more than five cytokines was characterized, we observed a more polyfunctional phenotype of NK cells from HLA-C1C1 patients (Fig. 4D). This analysis established that NK cells from HLA-C1C1 patients exhibited a higher output of multiple cytokines and greater cytokine polyfunctionality at the single-cell level, distinguished by a subset producing effector proteins (CCL-5, TNF-α, IFN-γ, MIP-1β, and IL-6). These findings together demonstrated that NK cells from CD patients with licensing genotypes were reprogrammed in a mosaic fashion for enhanced production of cytokines contributing to a chronic inflammatory state in vivo.

FIGURE 4.

NK cells from HLA-C1C1 patients contain a subset of NK cells polarized for proinflammatory cytokines production. (A) Univariate comparison of TNF-α production of NK cells from licensed (numbers 0919 and 1130, red) and unlicensed (numbers 0125 and 0811, blue) CD patients. The numbers in each graph indicate the percentage of microchambers that are positive for TNF-α signals. (B) Heat map of cytokine secretion capacity for all the cytokines and all the CD patients analyzed. Each row represents one cytokine, and each column represents the percentage of microchambers that are positive for the cytokine. The color scale shows the difference in SD. (C) PCA single NK cell measurements from the four CD patients. The percentage of variation explained by each component is shown in parentheses for each axis. The composition for each component is indicated on the left of the plots. (D) Bar graph of NK cell polyfunctionality. Different colors denote the percentages of single NK cells producing one, two, three, four, five, or more than five cytokines.

FIGURE 4.

NK cells from HLA-C1C1 patients contain a subset of NK cells polarized for proinflammatory cytokines production. (A) Univariate comparison of TNF-α production of NK cells from licensed (numbers 0919 and 1130, red) and unlicensed (numbers 0125 and 0811, blue) CD patients. The numbers in each graph indicate the percentage of microchambers that are positive for TNF-α signals. (B) Heat map of cytokine secretion capacity for all the cytokines and all the CD patients analyzed. Each row represents one cytokine, and each column represents the percentage of microchambers that are positive for the cytokine. The color scale shows the difference in SD. (C) PCA single NK cell measurements from the four CD patients. The percentage of variation explained by each component is shown in parentheses for each axis. The composition for each component is indicated on the left of the plots. (D) Bar graph of NK cell polyfunctionality. Different colors denote the percentages of single NK cells producing one, two, three, four, five, or more than five cytokines.

Close modal

A simple mechanistic explanation for the mosaic pattern of NK cytokine expression is the underlying developmental heterogeneity of NK cells. During NK cell development, KIRs are stochastically expressed, resulting in a composite of licensed and unlicensed NK cells in individuals with licensing genotypes (32). Accordingly, when such a subject is HLA-C1C1, KIR2DL3+ NK cells are licensed, and the KIR2DL3 NK cells are unlicensed. We therefore sorted licensed (CD3CD56dimKIR2DL3+KIR3DL1KIR2DL1) and unlicensed (CD3CD56dimKIR2DL3) subsets (>95% purity) and evaluated their cytokine production at the single-cell level using SCBCs. Compared with KIR2DL3 NK cells, KIR2DL3+KIR3DL1KIR2DL1 NK cells coexpressed elevated levels of CCL-5, MIP-1β, IFN-γ, and TNF-α (Fig. 5A). To look at the data from a different angle, the majority (65%) of KIR2DL3 NK cells did not secrete any cytokine. In contrast, 99% of KIR2DL3+KIR3DL1KIR2DL1 NK cells secreted at least one cytokine, with one-third expressing two cytokines (typically CCL-5+MIP-1β+), another third expressing three cytokines (mostly IFN-γ+MIP-1β+CCL-5+); a substantial fraction (10%) produced four cytokines (Fig. 5B).

FIGURE 5.

KIR2DL3+ NK cell subset is responsible for the enhanced proinflammatory cytokine production see in HLA-C1C1 individuals. Peripheral blood NK cells from an AA haplotype HLA-C1C1 healthy donor were sorted for KIR2DL3+KIR3DL1KIR2DL1 (licensed) and KIR2DL3 (unlicensed) NK subsets, stimulated with PMA/ionomycin, and analyzed using SCBC. (A) Two-dimensional scatter plot of representative cytokine production levels from licensed (red) and unlicensed (blue) NK cell subsets. Axis units are fluorescence intensity, and the value in each gated quadrant is the cell percentage. (B) Polyfunctionality plot showing the composition of NK subsets secreting zero, one, two, three, four, five, and more than five cytokines in licensed (red) and unlicensed (blue) NK cell subsets. The frequency for each major category is shown. (C) Hierarchical clustering of cytokine measurements from single licensed (red) and unlicensed (blue) NK cell subsets. Each column represents one single cell, and each row presents one cytokine. The color scale shows the difference in SD. Results are representative of three independent experiments.

FIGURE 5.

KIR2DL3+ NK cell subset is responsible for the enhanced proinflammatory cytokine production see in HLA-C1C1 individuals. Peripheral blood NK cells from an AA haplotype HLA-C1C1 healthy donor were sorted for KIR2DL3+KIR3DL1KIR2DL1 (licensed) and KIR2DL3 (unlicensed) NK subsets, stimulated with PMA/ionomycin, and analyzed using SCBC. (A) Two-dimensional scatter plot of representative cytokine production levels from licensed (red) and unlicensed (blue) NK cell subsets. Axis units are fluorescence intensity, and the value in each gated quadrant is the cell percentage. (B) Polyfunctionality plot showing the composition of NK subsets secreting zero, one, two, three, four, five, and more than five cytokines in licensed (red) and unlicensed (blue) NK cell subsets. The frequency for each major category is shown. (C) Hierarchical clustering of cytokine measurements from single licensed (red) and unlicensed (blue) NK cell subsets. Each column represents one single cell, and each row presents one cytokine. The color scale shows the difference in SD. Results are representative of three independent experiments.

Close modal

Analysis of ∼1500 single NK cells resolved them into two clusters (hierarchical clustering in Fig. 5C and PCA in Supplemental Fig. 2). One cluster, predominated by KIR2DL3+KIR3DL1KIR2DL1 NK cells was polarized toward a proinflammatory state (effector proteins such as TNF-α, IFN-γ, and chemokines). A second cluster, predominated by KIR2DL3 NK cells, was polarized toward a more regulatory state (including IL-4, TNF-β, TGF-β1, and IL-10). Taken together, licensing mediated by KIR2DL3/HLA-C1 interaction conferred proinflammatory immune mediator production program in NK cells.

To evaluate whether the cytokines produced by licensed NK cells could indeed promote CD4+ T cell proliferation, we neutralized IL-6, IFN-γ, TNF-α, or their combinations in NK-T cocultures (Fig. 6). Neutralization of TNF-α alone had a great impact on CD4+ T cell proliferation, and this effect was specific compared with IgG1κ isotype control. Neutralization of IL-6 or IFN-γ alone had measurable but modest effects, but their combination markedly reduced CD4+ T cell proliferation, suggesting synergistic interaction between them. We further evaluated T cell proliferation in the absence of NK cells, in which exogenous cytokines were added at 20 ng⋅ml−1, comparable to that produced by licensed NK cells (data not shown). IFN-γ or TNF-α had marginal effects, but the addition of IL-6 or all three greatly facilitated CD4+ T cell proliferation. This indicates that IL-6 might not be necessary to augment CD4+ T cell proliferation in the presence of other cytokines produced by licensed NK cells, but it was sufficient to carry the proliferating effect alone. These cytokine depletion and addition results demonstrated that CD4+ T cell proliferation mediated by NK cells does not rely solely on one particular cytokine but rather depends on the balance of multiple key cytokines.

FIGURE 6.

Neutralizing IFN-γ, TNF-α, and IL-6 in NK–T cell coculture ameliorated CD4+ T cell proliferation. NK and autologous CD4+ T cells were isolated from an AA haplotype licensed individual, stimulated with anti-CD3 and anti-CD28, and cocultured in 2 ng ml−1 (26 IU) IL-2 for 3 d. (A) Histograms of CD4+ T cell CFSE dilution without or with the indicated neutralizing Abs. The number in each histogram indicates the percentage of cells proliferated (gated on CD4+CFSE+ cells). (B) Bar plot of CD4+ T cells division number at NK/T = 1:1 from the AA haplotype healthy individual (mean ± SEM, n = 2–6, two-tailed Student t test, *p < 0.05, **p < 0.005, ***p < 0.0005). More than three experiments were performed.

FIGURE 6.

Neutralizing IFN-γ, TNF-α, and IL-6 in NK–T cell coculture ameliorated CD4+ T cell proliferation. NK and autologous CD4+ T cells were isolated from an AA haplotype licensed individual, stimulated with anti-CD3 and anti-CD28, and cocultured in 2 ng ml−1 (26 IU) IL-2 for 3 d. (A) Histograms of CD4+ T cell CFSE dilution without or with the indicated neutralizing Abs. The number in each histogram indicates the percentage of cells proliferated (gated on CD4+CFSE+ cells). (B) Bar plot of CD4+ T cells division number at NK/T = 1:1 from the AA haplotype healthy individual (mean ± SEM, n = 2–6, two-tailed Student t test, *p < 0.05, **p < 0.005, ***p < 0.0005). More than three experiments were performed.

Close modal

Th17 cells are crucial drivers for multiple chronic inflammatory diseases, including CD (33, 34), but there is little information about if or how NK cells might affect Th17 induction or activity. The foregoing results indicated that NK cells from HLA-C1C1 individuals are robust producers of several cytokines, notably IL-6, which is critical for Th17 differentiation (33, 35, 36). After validating conditions for cytokine induced formation of IL-17A– and IL-22–producing Th17 cells (Supplemental Fig. 3A), we determined whether the supernatant of NK cells from HLA-C1C1 healthy individuals could promote Th17 differentiation from total CD4+ T cells. Indeed, NK supernatants from an HLA-C1C1 healthy individual (AA haplotype), titrated into CD4+ T cell cultures, strongly induced the levels of IL-17A+, IL-22+, and IL-17A+IL-22+ T cells (Fig. 7A, 7B). These effects were observed with licensed NK supernatants alone, or in combination with IL-23, IL-1β, or both IL-1β and IL-23 (Supplemental Fig. 3B).

FIGURE 7.

Supernatant of licensed NK cells drives human Th17 cells differentiation in vitro. Freshly isolated CD4+ T cells were stimulated with anti-CD3 and anti-CD28 and cultured in the presence of indicated cytokine with or without licensed NK cell supernatants for 6–7 d. CD4+ T cells were expanded for another 6–7 d in 2 ng⋅ml−1 (26 IU) IL-2 with the same condition provided for priming. (A) Two-dimensional scatter plot of IL-17A and IL-22 intracellular production under the conditions indicated (gated on CD4+ cells). Numbers in each quadrant represent the percentage of cell in that quadrant. (B) Line plot of the abundances of IL-22+ (green triangle), IL-17A+ (purple cross), and IL-17A+IL-22+ (red square) populations at different amounts of NK supernatant. This result is representative of three independent experiments. (C) Bar plot of the percentages of IL-17A+ (left panel), IL-22+ (middle panel), and IL-17A+IL-22+ (right panel) CD4+ T cells after differentiating with 50% NK cell supernatants from three licensed healthy donors. M stands for media with the same amount of IL-2 used for NK 3-d culture. All assays have been supplemented with 50 ng⋅ml−1 IL-23 (n = 2, two-tailed Student t test, *p < 0.05) (0502 and 0911 are AA haplotype, 0711 has an extra KIR2DL2).

FIGURE 7.

Supernatant of licensed NK cells drives human Th17 cells differentiation in vitro. Freshly isolated CD4+ T cells were stimulated with anti-CD3 and anti-CD28 and cultured in the presence of indicated cytokine with or without licensed NK cell supernatants for 6–7 d. CD4+ T cells were expanded for another 6–7 d in 2 ng⋅ml−1 (26 IU) IL-2 with the same condition provided for priming. (A) Two-dimensional scatter plot of IL-17A and IL-22 intracellular production under the conditions indicated (gated on CD4+ cells). Numbers in each quadrant represent the percentage of cell in that quadrant. (B) Line plot of the abundances of IL-22+ (green triangle), IL-17A+ (purple cross), and IL-17A+IL-22+ (red square) populations at different amounts of NK supernatant. This result is representative of three independent experiments. (C) Bar plot of the percentages of IL-17A+ (left panel), IL-22+ (middle panel), and IL-17A+IL-22+ (right panel) CD4+ T cells after differentiating with 50% NK cell supernatants from three licensed healthy donors. M stands for media with the same amount of IL-2 used for NK 3-d culture. All assays have been supplemented with 50 ng⋅ml−1 IL-23 (n = 2, two-tailed Student t test, *p < 0.05) (0502 and 0911 are AA haplotype, 0711 has an extra KIR2DL2).

Close modal

Using the IL-23 plus NK supernatant condition, we analyzed NK cell supernatants from three different healthy subjects with a licensing genotype (AA haplotype, HLA-C1C1). All of them showed strong Th17 differentiation responses (Fig. 7C). Among the licensed NK-derived cytokines, IL-6 is a likely candidate to promote Th17 cell differentiation. However, blocking IL-6 alone didn’t detectably affect Th17 differentiation (Supplemental Fig. 3C). These findings demonstrate the capacity of licensed NK cells to secrete immune mediators that can strongly promote Th17 differentiation, either alone or synergistically with IL-23 and IL-1β.

Through a combination of advances in genotyping technologies, statistical advances and collaborative efforts, there have been spectacular advances in the understanding of the genetic contribution to complex diseases. Arguably, studies into the IBDs, CD, and ulcerative colitis have yielded the most successful results with >160 susceptibility loci now identified through a succession of genome-wide and more targeted approaches (34, 37, 38). The rapidity of gene discovery in IBD has far outpaced an understanding of both the functional and clinical consequences of associated variants and bridging this “genes to biology” gap requires significant investment and progress if the full benefits of genetic advances are to be realized. We and others have previously identified associations between IBD and genetic variation at the KIR locus (7, 13, 14). KIR genes are predominantly expressed by NK cells and are one element of the receptor repertoire controlling NK cell activation, proliferation, and effector functions that mediate surveillance and host defense for microbial infection and malignancy (10, 11). The relevance of this locus together with the role of NK cells in the development of IBD has recently been further highlighted with the publication of the IBD genome-wide association studies/Immunochip study (7).

Besides IBD, the genetic presence of strong NK licensing KIR/ligand pairs (KIR2DL3/HLA-C1 or KIR3DL1/HLA-Bw4) also affects several other important chronic inflammatory diseases: elevated susceptibility to CD, celiac disease, spondyloarthropathy, psoriatic arthritis; enhanced resolution of hepatitis C virus infection; and slower progression in HIV-1 infection (3945). Understanding the nature of KIR contribution to disease susceptibility or protection is crucial for developing diagnostic and treatment strategies. However, biologic study of KIR-mediated disease association has been challenging because of the polymorphic composition and functions of KIR haplotypes, and the independent assortment of their cognate HLA class I ligands. By focusing on the simplified AA haplotype, which “tag” most of the inhibitory KIRs that are involved in licensing and lack most of the activating KIRs, we were able to identify KIR-mediated licensing as a major mechanism to reprogram NK cell cytokine capacity. We further showed that, in accord with the distinct cytokines produced by licensed NK cells, they have the capacity to augment CD4+ T cell activation and Th17 differentiation, which provides a mechanistic basis for their genetic association to IBD and other chronic inflammatory diseases.

The distinct NK cytokine program induced by KIR licensing appears to be a genetic trait independent of disease status. Thus, NK cell licensing determined cytokine program was preserved in both CD and healthy cohorts (Figs. 24, Supplemental Figs. 1, 2); and functionally licensed NK cell cytokines from both CD and healthy subjects comparably augmented CD4+ T cell polarization (Figs. 1, 3). The exceptional breadth and proinflammatory cytokine profile of licensed NK cell is an important finding of this study, as well as the evidence that this cytokine production lowers the threshold for CD4+ T cell activation. Another striking finding was the selective capacity of licensed NK cell cytokines to efficiently drive IL-17A and IL-22 production. This is in part attributable to NK-derived IL-6; however, other NK-produced cytokines may also be involved, because in several culture conditions, Th17 polarization by NK cell supernatants exceeded that expected for IL-6 alone and blocking IL-6 alone did not affect Th17 differentiation (Fig. 7, Supplemental Fig. 3). Licensed NK cells synergize with IL-23 and IL-1β to facilitate Th17 differentiation, indicating that licensed NK cell secretory products can collaborate with other cells in the local tissue compartment (dendritic cells or macrophages) to promote a more proinflammatory environment shaping CD4+ or CD8+ T cell responses (46, 47). Further studies of unlicensed and licensed cells from healthy individuals will be required to validate and refine the effects of NK licensing in Th17 differentiation.

NK cells are not abundant and are functionally heterogeneous, posing significant challenges to understand individual cell behavior. We improved and used a single cell proteomics microchip for high-throughput, highly multiplexed, tailored analysis of cytokine expression capacity of NK cells. This microfluidic platform permits detection of ∼40 different protein products per individual cell and up to 1000 cells in a single experiment, and for the first time, to our knowledge, allows us to identify the striking distinctions between licensed and unlicensed NK cell subsets, and the commonality within each subset.

Finally, as the pathogenesis of CD is ultimately driven by intestinal lymphocytes; it is desirable to investigate properties of licensed NK cells resident in the gastrointestinal tract. However, the practicalities of such a study are quite difficult. Less than 10% of patients are genetically informative (KIR AA haplotype with HLA-C1/C1 genotypes); and even at a major IBD clinical center, intestinal resections from 10 patients would require 2 y to accrue. The alternative of colonscopic biopsy sampling is also technically unsuitable. Because of the low abundance of CD3-CD56+ NK cells in the intraepithelial and lamina propria compartments [∼18.5 and ∼10%, respectively (48, 49)], and low cellular yield per biopsy [1–2 million lymphocytes per 2-mm2 biopsy (50)], ∼20 biopsies from each patient are required for a minimal experiment, which is beyond the number permitted for research sampling. We also note that IBD is a systemic disease with >40% of IBD patients having extraintestinal manifestations. In this context, the study of NK cells from peripheral compartments is relevant to IBD biology.

Bridging the “gene to biology” and “bench to bedside” divides is one of the major challenges currently facing researchers. Our study addresses this challenge through mechanistic finding of the proinflammatory role of licensed NK cells on adaptive immunity. This offers a fresh biologic diagram accounting for the impact of KIR-HLA genetics on IBD and other chronic inflammatory diseases.

This work was supported by National Institutes of Health Grants PO1DK46763 (to S.R.T., D.P.B.M., and J.B.), CA119347 (to J.R.H.), 5 UO1 AI067068 (to H.A.E., E.A.T., and D.P.B.M.), DK062413 and DK046763-19 (to D.P.B.M.), and UL1TR000124 (to S.R.T., D.P.B.M., and J.B.) and the Cedars-Sinai F. Widjaja Inflammatory Bowel and Immunobiology Institute Research Fund. Project investigators were supported by the Helmsley Charitable Trust (to D.P.B.M.) and the European Union (to D.P.B.M.). This research was performed with material support provided by the Immune Tolerance Network, an international clinical research consortium headquartered at the University of California, San Francisco, and supported by the National Institute of Allergy and Infectious Diseases and the Juvenile Diabetes Research Foundation.

The online version of this article contains supplemental material.

Abbreviations used in this article:

CD

Crohn’s disease

IBD

inflammatory bowel disease

KIR

killer Ig-like receptor

PCA

principal component analysis

SCBC

single-cell barcode chip

UCLA

University of California, Los Angeles.

1
Hesslein
D. G.
,
Lanier
L. L.
.
2011
.
Transcriptional control of natural killer cell development and function.
Adv. Immunol.
109
:
45
85
.
2
Elliott
J. M.
,
Yokoyama
W. M.
.
2011
.
Unifying concepts of MHC-dependent natural killer cell education.
Trends Immunol.
32
:
364
372
.
3
Vivier
E.
,
Tomasello
E.
,
Baratin
M.
,
Walzer
T.
,
Ugolini
S.
.
2008
.
Functions of natural killer cells.
Nat. Immunol.
9
:
503
510
.
4
Vivier
E.
,
Raulet
D. H.
,
Moretta
A.
,
Caligiuri
M. A.
,
Zitvogel
L.
,
Lanier
L. L.
,
Yokoyama
W. M.
,
Ugolini
S.
.
2011
.
Innate or adaptive immunity? The example of natural killer cells.
Science
331
:
44
49
.
5
Bashirova
A. A.
,
Thomas
R.
,
Carrington
M.
.
2011
.
HLA/KIR restraint of HIV: surviving the fittest.
Annu. Rev. Immunol.
29
:
295
317
.
6
Khakoo
S. I.
,
Carrington
M.
.
2006
.
KIR and disease: a model system or system of models?
Immunol. Rev.
214
:
186
201
.
7
Jostins
L.
,
Ripke
S.
,
Weersma
R. K.
,
Duerr
R. H.
,
McGovern
D. P.
,
Hui
K. Y.
,
Lee
J. C.
,
Schumm
L. P.
,
Sharma
Y.
,
Anderson
C. A.
, et al
.
2012
.
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Nature
491
:
119
124
.
8
Hall
L. J.
,
Murphy
C. T.
,
Quinlan
A.
,
Hurley
G.
,
Shanahan
F.
,
Nally
K.
,
Melgar
S.
.
2013
.
Natural killer cells protect mice from DSS-induced colitis by regulating neutrophil function via the NKG2A receptor.
Mucosal Immunol.
6
:
1016
1026
.
9
Saha
S.
,
Jing
X.
,
Park
S. Y.
,
Wang
S.
,
Li
X.
,
Gupta
D.
,
Dziarski
R.
.
2010
.
Peptidoglycan recognition proteins protect mice from experimental colitis by promoting normal gut flora and preventing induction of interferon-gamma.
Cell Host Microbe
8
:
147
162
.
10
Lanier
L. L.
2005
.
NK cell recognition.
Annu. Rev. Immunol.
23
:
225
274
.
11
Fauriat
C.
,
Ivarsson
M. A.
,
Ljunggren
H. G.
,
Malmberg
K. J.
,
Michaëlsson
J.
.
2010
.
Education of human natural killer cells by activating killer cell immunoglobulin-like receptors.
Blood
115
:
1166
1174
.
12
Du
Z.
,
Gjertson
D. W.
,
Reed
E. F.
,
Rajalingam
R.
.
2007
.
Receptor-ligand analyses define minimal killer cell Ig-like receptor (KIR) in humans.
Immunogenetics
59
:
1
15
.
13
Hollenbach
J. A.
,
Ladner
M. B.
,
Saeteurn
K.
,
Taylor
K. D.
,
Mei
L.
,
Haritunians
T.
,
McGovern
D. P.
,
Erlich
H. A.
,
Rotter
J. I.
,
Trachtenberg
E. A.
.
2009
.
Susceptibility to Crohn’s disease is mediated by KIR2DL2/KIR2DL3 heterozygosity and the HLA-C ligand.
Immunogenetics
61
:
663
671
.
14
Wilson
T. J.
,
Jobim
M.
,
Jobim
L. F.
,
Portela
P.
,
Salim
P. H.
,
Rosito
M. A.
,
Damin
D. C.
,
Flores
C.
,
Peres
A.
,
Machado
M. B.
, et al
.
2010
.
Study of killer immunoglobulin-like receptor genes and human leukocyte antigens class I ligands in a Caucasian Brazilian population with Crohn’s disease and ulcerative colitis.
Hum. Immunol.
71
:
293
297
.
15
Jones
D. C.
,
Edgar
R. S.
,
Ahmad
T.
,
Cummings
J. R.
,
Jewell
D. P.
,
Trowsdale
J.
,
Young
N. T.
.
2006
.
Killer Ig-like receptor (KIR) genotype and HLA ligand combinations in ulcerative colitis susceptibility.
Genes Immun.
7
:
576
582
.
16
Yokoyama
W. M.
,
Kim
S.
.
2006
.
How do natural killer cells find self to achieve tolerance?
Immunity
24
:
249
257
.
17
Anfossi
N.
,
André
P.
,
Guia
S.
,
Falk
C. S.
,
Roetynck
S.
,
Stewart
C. A.
,
Breso
V.
,
Frassati
C.
,
Reviron
D.
,
Middleton
D.
, et al
.
2006
.
Human NK cell education by inhibitory receptors for MHC class I.
Immunity
25
:
331
342
.
18
Fauriat
C.
,
Long
E. O.
,
Ljunggren
H. G.
,
Bryceson
Y. T.
.
2010
.
Regulation of human NK-cell cytokine and chemokine production by target cell recognition.
Blood
115
:
2167
2176
.
19
Hollenbach
J. A.
,
Nocedal
I.
,
Ladner
M. B.
,
Single
R. M.
,
Trachtenberg
E. A.
.
2012
.
Killer cell immunoglobulin-like receptor (KIR) gene content variation in the HGDP-CEPH populations.
Immunogenetics
64
:
719
737
.
20
Yawata
M.
,
Yawata
N.
,
Draghi
M.
,
Partheniou
F.
,
Little
A. M.
,
Parham
P.
.
2008
.
MHC class I-specific inhibitory receptors and their ligands structure diverse human NK-cell repertoires toward a balance of missing self-response.
Blood
112
:
2369
2380
.
21
Neurath
M. F.
,
Finotto
S.
,
Glimcher
L. H.
.
2002
.
The role of Th1/Th2 polarization in mucosal immunity.
Nat. Med.
8
:
567
573
.
22
Bouma
G.
,
Strober
W.
.
2003
.
The immunological and genetic basis of inflammatory bowel disease.
Nat. Rev. Immunol.
3
:
521
533
.
23
Kim
S.
,
Sunwoo
J. B.
,
Yang
L.
,
Choi
T.
,
Song
Y. J.
,
French
A. R.
,
Vlahiotis
A.
,
Piccirillo
J. F.
,
Cella
M.
,
Colonna
M.
, et al
.
2008
.
HLA alleles determine differences in human natural killer cell responsiveness and potency.
Proc. Natl. Acad. Sci. USA
105
:
3053
3058
.
24
Shi
F. D.
,
Van Kaer
L.
.
2006
.
Reciprocal regulation between natural killer cells and autoreactive T cells.
Nat. Rev. Immunol.
6
:
751
760
.
25
Narni-Mancinelli
E.
,
Jaeger
B. N.
,
Bernat
C.
,
Fenis
A.
,
Kung
S.
,
De Gassart
A.
,
Mahmood
S.
,
Gut
M.
,
Heath
S. C.
,
Estellé
J.
, et al
.
2012
.
Tuning of natural killer cell reactivity by NKp46 and Helios calibrates T cell responses.
Science
335
:
344
348
.
26
Martín-Fontecha
A.
,
Thomsen
L. L.
,
Brett
S.
,
Gerard
C.
,
Lipp
M.
,
Lanzavecchia
A.
,
Sallusto
F.
.
2004
.
Induced recruitment of NK cells to lymph nodes provides IFN-γ for T(H)1 priming.
Nat. Immunol.
5
:
1260
1265
.
27
Assarsson
E.
,
Kambayashi
T.
,
Schatzle
J. D.
,
Cramer
S. O.
,
von Bonin
A.
,
Jensen
P. E.
,
Ljunggren
H. G.
,
Chambers
B. J.
.
2004
.
NK cells stimulate proliferation of T and NK cells through 2B4/CD48 interactions.
J. Immunol.
173
:
174
180
.
28
Zingoni
A.
,
Sornasse
T.
,
Cocks
B. G.
,
Tanaka
Y.
,
Santoni
A.
,
Lanier
L. L.
.
2004
.
Cross-talk between activated human NK cells and CD4+ T cells via OX40-OX40 ligand interactions.
J. Immunol.
173
:
3716
3724
.
29
Hanna
J.
,
Gonen-Gross
T.
,
Fitchett
J.
,
Rowe
T.
,
Daniels
M.
,
Arnon
T. I.
,
Gazit
R.
,
Joseph
A.
,
Schjetne
K. W.
,
Steinle
A.
, et al
.
2004
.
Novel APC-like properties of human NK cells directly regulate T cell activation.
J. Clin. Invest.
114
:
1612
1623
.
30
Ma
C.
,
Fan
R.
,
Ahmad
H.
,
Shi
Q.
,
Comin-Anduix
B.
,
Chodon
T.
,
Koya
R. C.
,
Liu
C. C.
,
Kwong
G. A.
,
Radu
C. G.
, et al
.
2011
.
A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells.
Nat. Med.
17
:
738
743
.
31
Fan
R.
,
Vermesh
O.
,
Srivastava
A.
,
Yen
B. K.
,
Qin
L.
,
Ahmad
H.
,
Kwong
G. A.
,
Liu
C. C.
,
Gould
J.
,
Hood
L.
,
Heath
J. R.
.
2008
.
Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood.
Nat. Biotechnol.
26
:
1373
1378
.
32
Valiante
N. M.
,
Uhrberg
M.
,
Shilling
H. G.
,
Lienert-Weidenbach
K.
,
Arnett
K. L.
,
D’Andrea
A.
,
Phillips
J. H.
,
Lanier
L. L.
,
Parham
P.
.
1997
.
Functionally and structurally distinct NK cell receptor repertoires in the peripheral blood of two human donors.
Immunity
7
:
739
751
.
33
McGeachy
M. J.
,
Cua
D. J.
.
2008
.
Th17 cell differentiation: the long and winding road.
Immunity
28
:
445
453
.
34
Franke
A.
,
McGovern
D. P.
,
Barrett
J. C.
,
Wang
K.
,
Radford-Smith
G. L.
,
Ahmad
T.
,
Lees
C. W.
,
Balschun
T.
,
Lee
J.
,
Roberts
R.
, et al
.
2010
.
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci.
Nat. Genet.
42
:
1118
1125
.
35
Acosta-Rodriguez
E. V.
,
Napolitani
G.
,
Lanzavecchia
A.
,
Sallusto
F.
.
2007
.
Interleukins 1β and 6 but not transforming growth factor-β are essential for the differentiation of interleukin 17-producing human T helper cells.
Nat. Immunol.
8
:
942
949
.
36
Wilson
N. J.
,
Boniface
K.
,
Chan
J. R.
,
McKenzie
B. S.
,
Blumenschein
W. M.
,
Mattson
J. D.
,
Basham
B.
,
Smith
K.
,
Chen
T.
,
Morel
F.
, et al
.
2007
.
Development, cytokine profile and function of human interleukin 17-producing helper T cells.
Nat. Immunol.
8
:
950
957
.
37
Anderson
C. A.
,
Boucher
G.
,
Lees
C. W.
,
Franke
A.
,
D’Amato
M.
,
Taylor
K. D.
,
Lee
J. C.
,
Goyette
P.
,
Imielinski
M.
,
Latiano
A.
, et al
.
2011
.
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Nat. Genet.
43
:
246
252
.
38
McGovern
D. P.
,
Gardet
A.
,
Törkvist
L.
,
Goyette
P.
,
Essers
J.
,
Taylor
K. D.
,
Neale
B. M.
,
Ong
R. T.
,
Lagacé
C.
,
Li
C.
, et al
.
2010
.
Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
Nat. Genet.
42
:
332
337
.
39
Martin
M. P.
,
Nelson
G.
,
Lee
J. H.
,
Pellett
F.
,
Gao
X.
,
Wade
J.
,
Wilson
M. J.
,
Trowsdale
J.
,
Gladman
D.
,
Carrington
M.
.
2002
.
Cutting edge: susceptibility to psoriatic arthritis: influence of activating killer Ig-like receptor genes in the absence of specific HLA-C alleles.
J. Immunol.
169
:
2818
2822
.
40
Moodie
S. J.
,
Norman
P. J.
,
King
A. L.
,
Fraser
J. S.
,
Curtis
D.
,
Ellis
H. J.
,
Vaughan
R. W.
,
Ciclitira
P. J.
.
2002
.
Analysis of candidate genes on chromosome 19 in coeliac disease: an association study of the KIR and LILR gene clusters.
Eur. J. Immunogenet.
29
:
287
291
.
41
Chan
A. T.
,
Kollnberger
S. D.
,
Wedderburn
L. R.
,
Bowness
P.
.
2005
.
Expansion and enhanced survival of natural killer cells expressing the killer immunoglobulin-like receptor KIR3DL2 in spondylarthritis.
Arthritis Rheum.
52
:
3586
3595
.
42
Brodin
P.
,
Lakshmikanth
T.
,
Kärre
K.
,
Höglund
P.
.
2012
.
Skewing of the NK cell repertoire by MHC class I via quantitatively controlled enrichment and contraction of specific Ly49 subsets.
J. Immunol.
188
:
2218
2226
.
43
Zhi
D.
,
Sun
C.
,
Sedimbi
S. K.
,
Luo
F.
,
Shen
S.
,
Sanjeevi
C. B.
.
2011
.
Killer cell immunoglobulin-like receptor along with HLA-C ligand genes are associated with type 1 diabetes in Chinese Han population.
Diabetes Metab. Res. Rev.
27
:
872
877
.
44
Mehers
K. L.
,
Long
A. E.
,
van der Slik
A. R.
,
Aitken
R. J.
,
Nathwani
V.
,
Wong
F. S.
,
Bain
S.
,
Gill
G.
,
Roep
B. O.
,
Bingley
P. J.
,
Gillespie
K. M.
.
2011
.
An increased frequency of NK cell receptor and HLA-C group 1 combinations in early-onset type 1 diabetes.
Diabetologia
54
:
3062
3070
.
45
Shastry
A.
,
Sedimbi
S. K.
,
Rajalingam
R.
,
Nikitina-Zake
L.
,
Rumba
I.
,
Wigzell
H.
,
Sanjeevi
C. B.
.
2008
.
Combination of KIR 2DL2 and HLA-C1 (Asn 80) confers susceptibility to type 1 diabetes in Latvians.
Int. J. Immunogenet.
35
:
439
446
.
46
Raué
H. P.
,
Beadling
C.
,
Haun
J.
,
Slifka
M. K.
.
2013
.
Cytokine-mediated programmed proliferation of virus-specific CD8+ memory T cells.
Immunity
38
:
131
139
.
47
Richer
M. J.
,
Nolz
J. C.
,
Harty
J. T.
.
2013
.
Pathogen-specific inflammatory milieux tune the antigen sensitivity of CD8+ T cells by enhancing T cell receptor signaling.
Immunity
38
:
140
152
.
48
Eiras
P.
,
Leon
F.
,
Camarero
C.
,
Lombardia
M.
,
Roldan
E.
,
Bootello
A.
,
Roy
G.
.
2000
.
Intestinal intraepithelial lymphocytes contain a CD3CD7+ subset expressing natural killer markers and a singular pattern of adhesion molecules.
Scand. J. Immunol.
52
:
1
6
.
49
Sips
M.
,
Sciaranghella
G.
,
Diefenbach
T.
,
Dugast
A. S.
,
Berger
C. T.
,
Liu
Q.
,
Kwon
D.
,
Ghebremichael
M.
,
Estes
J. D.
,
Carrington
M.
, et al
.
2012
.
Altered distribution of mucosal NK cells during HIV infection.
Mucosal Immunol.
5
:
30
40
.
50
León
F.
,
Roldán
E.
,
Sanchez
L.
,
Camarero
C.
,
Bootello
A.
,
Roy
G.
.
2003
.
Human small-intestinal epithelium contains functional natural killer lymphocytes.
Gastroenterology
125
:
345
356
.

The authors have no financial conflicts of interest.

Supplementary data