Natural Killer Cell Receptors Research Articles

Gene and genotype frequencies of immunoglobulin-like natural killer cell receptors in the population of Samara region

Background. The using of killer-cell immunoglobulin-like receptor (KIR) composition data is of increasing interest in clinical practice to select an optimal donor for allogeneic hematopoietic stem cell transplantation for treatment of hematologic malignancies to reduce graft versus host disease and the risk of relapse. It is also of interest to study the frequencies of KIR genes and genotypes in different populations. For the Russian Federation, KIR gene and genotype frequencies have been described for only a few relatively small samples and have not been fully studied. The study of KIR gene and genotype frequencies has not been conducted for the Samara region population to date.Aim. To study the frequencies of KIR genes and genotypes in the population of Samara region and to compare the data with previously described Russian populations.Materials and methods. To study the frequencies of KIR genes and genotypes, molecular genetic typing of 142 CBUs from the public cord blood bank of the Samara Regional Medical Centre “Dynasty” was performed. Molecular genetic typing of KIR genes was performed by polymerase chain reaction with sequence-specific primers with subsequent visualization of products in agarose gel. 16 KIR genes and pseudogenes were analyzed: 2DL1, 2DL2, 2DL3, 3DL1, 3DL2, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DS1, 2DP1, 3DL3, 2DL4, 2DL5, 3DP1. KIR gene frequencies were determined by direct counting. Genotypes were determined using Allele Frequencies database. A determination B-content group was performed using the Donor KIR B-content group calculator. Statistical analysis was performed using the χ2 test.Results. The highest frequency of KIR inhibitory genes was found for KIR2DL1 (98.6 %), KIR3DL1 (98.6 %), KIR2DL3 (96.5 %), KIR2DL5 (46.5 %), and KIR2DL2 (34.5 %). The most frequent among the activating receptor genes was KIR2DS4 (89.4 %), the frequencies of other KIR activating genes were KIR2DS2 – 45.1 %, KIR2DS1 – 35.9 %, KIR2DS3 33.8 %, and KIR2DS5 – 26.1 %. Comparative analysis of KIR gene frequencies in the population of Samara region and other Russian populations revealed certain differences. Significant differences in the frequencies of occurrence were found for KIR2DL3, KIR2DS4, KIR2DL2, KIR2DL5, KIR2DS3, KIR2DS5, as well as KIR2DP1 and KIR3DP1. Examination of 142 samples revealed 45 different genotypes: AA genotypes were detected in 30 % and Bx genotypes in 70 % of cases. AA genotype ID195 with a frequency of 5.6 % was detected, which has not been previously described in Russian populations. Among the Samara region population sample, only 3.5 % had the “best” status, 20.4 % had the “better” status, and 76.1 % had the “neutral” status of the B-content.Conclusion. The results obtained in this sample on the frequencies of KIR genes and genotypes differ from the previously published data for the Russian Federation. Of interest is the finding of a greater diversity of genotypes among a rather small study group, the detection of an atypical ID195 genotype, and the difference in the representation of B-content groups. The analysis of KIR genotypes in the population of Samara region can be used in the selection of optimal CBU and hematopoietic cell/bone marrow donors in addition to HLA typing. Studying the frequency distribution of KIR and HLA genes and genotypes can play a role in the study of fundamental aspects of human immunology and population genetics.

Effects of homo‐ and heterozygous TREM2 mutations on natural killer cell activity

AbstractBackgroundNasu‐Hakola disease (NHD) is a rare genetic neurodegenerative disorder characterised by progressive presenile dementia and bone cysts. Dysfunctions in myeloid‐derived innate immune cells such as microglia due to loss‐of‐function mutations in the TREM2 (trigger receptor 2 expressed on myeloid cells) gene cause the clinical manifestations. Heterozygous carriers have strongly increased risk of developing Alzheimer’s Disease but do not present with NHD symptoms. TREM2 is associated with DAP12 protein, which contains an immunoreceptor tyrosine‐based activation motif that is structurally similar to natural killer (NK) cell receptors. In this study, we aimed to analyse the effects of TREM2 mutation and its effect on the peripheral immune system represented by NK cell functions.MethodSix patients with NHD with a defined homozygous TREM2 mutation, 7 carriers with heterozygous TREM2 mutations and 10 age‐ and gender‐matched controls were included. NK cell subsets, KIR expressions (NKG2A, NKG2D, NKp46), cytotoxic activity (CD107a, Perforin, Granzyme A) and cytokine secretions (IL‐4, IFN‐γ, TNF‐α, IL‐10, IL‐17, TGF‐β) were analysed by flow cytometry.ResultCD3−CD56dimCD16− (p = 0.003) subsets were found to be increased in the NHD group compared to carriers. Activating C‐type lectin receptor NKG2D expression was increased in CD8+ (p = 0.003) NK cell subsets in the NHD group. Inhibiting C‐type lectin receptor NKG2A expression was increased in total (p = 0.011) as well as CD8+ (p = 0.007) NK cell subsets in carriers compared to controls. In total NK cells, intracellular TNF‐α (p = 0.005) and TGF‐β (p = 0.013) levels were decreased, IL‐17 (p = 0.05) and IL‐4 (p = 0.005) levels were increased in the NHD group. When NK cells were grouped due to their CD8 expression, TNF‐α levels were decreased, and IL‐17 levels were increased in both subsets in the NHD group. Cytotoxic activity showed no differentiation in both unstimulated and K562 stimulated conditions between groups.ConclusionUnlike previous case series, NK cell ratios did not differ between groups. Over‐expression of inhibiting receptors in the carriers group, unlike high levels of activating receptors in the NHD, might explain the lack of symptoms in the carriers. The increased ratio of CD3−CD56dimCD16− NK cell subsets that overexpress inhibitory checkpoints might explain the low levels of pro‐inflammatory cytokines in the NHD group.

Role of non-canonical T cells in homeostasis and pathology

In addition to the subsets of T lymphocytes and innate lymphocytes (innate lymphoid cells), the well-known players in adaptive immunity, there is an intermediate group of lymphocytes (innate-like cells) that already possess the T cell receptor, but with a restricted repertoire. This group includes γδT cells, subsets of type I and II NKT cells carrying both T cell receptor and NK-cell receptors, and mucosal-associated invariant T (MAIT) cells. The development of innate-like cells occurs in the thymus, but their positive and negative selection takes place without the participation of thymic epithelial cells. A distinctive feature is that innate-like cells acquire an effector phenotype already in the thymus, and therefore do not require complex activation reactions during antigen recognition. Upon exit from the thymus, noncanonical T cells express chemokine receptors, allowing them to migrate into barrier tissues at an early age. A characteristic feature of the T cell receptor innate-like cells is the recognition of non-peptide antigens presented in non-polymorphic histocompatibility molecules (MHC-Ib). This type of molecule includes the CD1 a/b/c/d/e molecule and the MR1 molecule. These molecules present lipid, glycolipid antigens and metabolites of B vitamins, synthesized by various representatives of the microbiota. The presence of functionally different subpopulations of innate-like cells with an activated phenotype allows them to quickly respond to the antigen by producing cytokines typical of Th1, Th2, Th17. They also exhibit cytotoxic and immunoregulatory activity. These cells are actively involved in regulation of barrier tissue homeostasis and interaction with microbiota. They synthesize growth factors for epithelial cells, fibroblasts, and vascular endothelium, which are required for regeneration of damaged tissues. They also participate in anti-infectious defense, directing the development of the immune response. Moreover, they have been found to be involved in many autoimmune diseases. The special functions of innate-like cells make them a promising target for therapeutic interventions. It has been shown that antibiotics, salicylates and some other well-known drugs exert certain effects on the innate-like cells. Different dietary options also affect the activity of these cells.

Natural Killer Cells Are Active Against Myeloma, Leukemia or Lymphoma Cells with Loss of Tumor Suppressor Genes

The therapeutic targeting of tumor cells with loss of function (LOF) for tumor suppressor genes (TSGs) is challenging across cancers, including hematologic neoplasias, because pharmacological mechanisms to restore the function(s) of such genes are not readily feasible, in contrast to e.g., inhibition of oncogenic drivers. We reasoned, however, that, although LOF for TSGs leads to de-repressed growth of neoplastic hematopoietic cells, it may not necessarily protect them from immune attack. We thus explored the hypothesis that CRISPR-based loss of function of TSGs in cells from multiple myeloma (MM), leukemias or lymphoma may still be associated with substantial response to immune effector cells such as NK cells, which have the advantage to kill tumor cells across HLA barriers. We have conducted CRISPR-based studies in 7 cell lines that represent different hematologic malignancies and different levels of sensitivity to natural killer (NK) cells, namely the B-cell lymphoma (SUDHL4), precursor B cell acute lymphoblastic leukemia (NALM6), multiple myeloma (MM1.S, LP1, KMS11), chronic myeloid leukemia (K562), and acute myeloid leukemia (MOLM14). In these genome-scale or focused CRISPR screens for LOF (CRISPR-based gene editing) or gain of function (GOF, CRISPR activation), the blood cancer lines were exposed to allogeneic donor-derived NK cells (vs. control cultures without NK cells). We evaluated the performance of genes known to represent recurrent TSGs based on genomic data of patient samples or cell lines; as well as candidate TSGs, based on results from genome-scale CRISPR gene editing screens (e.g., CERES or CHRONOS scores >0.4 in multiple DepMap releases and TPM>1 [RNA-seq]) in the same cell lines as the NK cell resistance screens. These analyses sought to identify any TSGs whose LOF may potentially alter the response of blood cancer cells to NK cells. We also evaluated genes identified as top recurrent TSGs in patient samples from MM and other hematologic neoplasias (e.g., based on prior genomic studies). On aggregate, we evaluated a collection of known and recurrent TSGs (e.g., PTEN, TP53, RB1, CDKN2C, CDKN1B, TENT5C/FAM46C) as well as other, previously underappreciated candidate genes with TSG properties in hematologic neoplasias (e.g., HIF1A, DEPDC5). Perturbation of none of these genes was identified to meet criteria for association with significant resistance to allogeneic donor-derived NK cells (e.g., log2FC>1.0, at least 3-4 sgRNAs with enrichment upon CRISPR KO or depletion with CRISPR activation, p-value <0.05, enrichment rank <100, based on rank aggregation algorithm) in any of the MM, leukemia or lymphoma cell lines examined in LOF or GOF CRISPR screens for NK cell resistance. In fact, for a limited set of cases (e.g., PTEN in KMS11 cells), KO of a TSG was associated with sensitization to NK cell treatment. To probe the mechanistic basis for this lack of effect of TSG loss, we examined the molecular sequelae of CRISPR-based KO for one of these recurrent TSGs, PTEN, by performing scRNAseq using the CROP-seq platform. Pools of MM1.S and LP1 cells expressing sgRNAs targeting select hits from our CRISPR screens and also PTEN were co-cultured with NK cells for 24 h or left untreated, followed by scRNA-seq and sgRNA detection, differential gene-expression analysis. We observed in these studies that the transcriptional changes induced in MM cells by KO of PTEN included limited, if any, changes in the expression of key genes involved in regulation of NK cell responses of tumor cells, e.g., ligands for activating or inhibitor receptors in NK cells, death receptors (e.g., TRAIL, Fas) or their downstream effectors/regulators or other molecules identified from our aforementioned genome-scale and focused CRISPR LOF and GOF studies. Notably, our in-house results from studies of NK exposure of cell lines from hematologic neoplasias are concordant with results for these TSGs in CRISPR screens of non-hematological cancer cells treated with cytotoxic T-cells (e.g., 4T1 or RENCA cells; GSE149933). Overall, our observations indicate that MM, leukemia or lymphoma cells that become deficient for diverse TSGs based on CRISPR-based gene editing are equally responsive to NK cells as their TSG-proficient counterparts. NK cell-based therapies may thus be a promising approach to target TSG-deficient hematologic malignancies for which specific pharmacological therapies are not currently available.

A Scalable, Off-the-Shelf, and Cost-Effective NK Cell Manufacturing Platform for Developing NK Cell-Based Immunotherapy

Natural killer (NK) cells are innate lymphocytes that play a key role in the control of infection and malignancy. NK cells are potent killers of target cells and act in an MHC-independent manner, enabling their application as allogenic therapy for cancer. Human iPSCs are pluripotent with the ability to self-renew, thus providing an inexhaustible source for deriving NK cells. With a two-tiered cell bank system, we can manufacture NK cells with more homogeneity between batches. In principle, one single iPSC clone-derived master cell bank and working cell banks can support the life cycle of an affordable, off-the-shelf NK cell product. We developed a robust stepwise protocol for large-scale generation of high-purity NK cells from human iPSCs without the cell isolation procedure. First, human iPSCs formed embryoid bodies and then were differentiated into highly purified (>98.0%) CD34 + CD43 + hematopoietic stem and progenitor cells (HSPCs) using a combination of cytokines and small molecles such as BMP-4, VEGF, BFGF, SCF, FLT-3 and ascorbic acid. During this period, we observed up to an 180-fold cell increase in the number of HSPCs compared with human iPSCs. Second, these HSPCs were differentiated into NK cells with FLT3, SCF, IL-3, IL-7, and IL-15 etc., with cell number increased approximately 9000-fold compared with iPSCs. In the final step, iPSC-derived NK cells were further expanded up to 8000-fold which enable us to produce 1E12 NK cells from less than 1 million iPSCs. After expansion, iNK cells became more homogenous and exhibited a more mature phenotype. More than 99.0% of cells expressed both CD45 and CD56, and more than 70% expressed CD16. The expression of activating and co-stimulatory receptors (NKG2D, NKp46,NKp44, NKp30, CD244 and CD226) of NK cells was also high in these iNK cells. Intrestingly, the cells exhibited robust anti-tumor efficacy against K562 (chronic myelogenous leukemia), RPMI 8226 (multiple myeloma). Furthermore, the cryopreserved iNK cells demonstrated dramatic cytotoxicity to U-87 MG cells (malignant gliomas) in 2D culture and the tumor organoid, indicating that iNK cells derived from our protocol can be used as off-the-shelf therapy for both hematological and solid tumors. We also observed that these iNK cells had variable cytotoxicity in other tumors. For example, our iNK were not obviously cytotoxic to the NCI-H929 cell line, derived from a plasmacytoma myeloma patient and expressing BCMA at a high level. To improve the specific cytotoxicity of NK cells to NCI-H929 cells, we transduced a anti-BCMA CAR to the donor iPSC. Following differentiation, the CAR-transduced iNK cells showed approximately 6-fold cytotoxicity compared with WT iNK. (Figure 1) Collectively, our serum-free and strom cell-free NK cell generation produre from human iPSCs provides a scalable, consistent, off-the-shelf and cost-effective NK/CAR-NK cell manufacturing platform for clinical application and NK cell-based immunotherapies.

Day 100 Inhibitory KIR2DL2 and Activating NKp30 Natural Killer Cell Receptors Predicts Survival Post-Autologous Stem Cell Transplantation in Lymphomas

Introduction: Our group previously published that the infusion autograft inhibitor KIR2DL2 (CD158b+CD337-) and activating NKp30 (CD158b- CD337+) Natural killer (NK) cells receptors were predictors of clinical outcomes in lymphoma patients undergoing autologous peripheral blood hematopoietic stem cell transplantation (APBHSCT) (Porrata et al. Leukemia Research 2019; 81: 1-9). To assess if these subsets of NK cells still hold clinical relevance, we set up to investigate their prognostic ability to predict clinical outcomes at Day 100 post-APBHSCT. Methods: 107 lymphoma patients who participated in our double-blind phase III trail (Porrata et al, Biology of Blood and Marrow Transplantation 2016; 22(6); 1017-1023) and had clinical assessment at Day 100 post-APBHSCT were included in this study. Nkp30 and KIR2DL2 at Day 100 were assessed by flow cytometry analysis. Results: With a median follow-up for the entire cohort from Day 100 was 94.7 months (range: 4.83-158.1 months). Figure 1 shows the overall survival (OS) and progression-free survival (PFS) based on the absolute numbers of KIR2DL2 and Nkp30 NK cells. At Day 100, patients with a KIR2DL2 < 0.08 and Nkp30 ≥0.19 experienced superior OS and PFS compared with patients with a Day 100 KIR2DLD2 ≥0.08 and NKp30 < 0.19. In the multivariate analysis both the KIR2DL2 [OS: HR = 1.767, 95%CI, 1.302-30.31, p < 0.04; and PFS: HR = 2.663, 95%CI, 1.108-6.403, p < 0.03] and Nkp30 [OS: HR = 2.594, 95% CI, 1.239-5.432, p < 0.01; and PFS: HR = 3.676, 95% CI, 1.875-7.206, p < 0.01] were independent predictors for OS and PFS. Conclusion: Day 100 inhibitory KIR2DL2 and activating NKp30 NK cells are prognostic immune-biomarkers in lymphoma patients undergoing APBHSCT.

A High Percentage of DNAM-1+ and Low Percentage of Tactile+ NK Cells at Diagnosis Correlate with Complete Response and Survival in AML: A Sub-Analysis of the Ven-a-Qui Pethema Trial

Background: Natural killer (NK) immune status in Acute Myeloid Leukemia (AML) could influence therapeutic results and natural history of the disease. Objectives: In the phase I/II VEN-A-QUI (Clinical trials NCT04687761) clinical trial for unfit newly diagnosed AML patients (venetoclax+Quizartinib+azacytidine or low-dose cytarabine), it was planned a prospective study of NK populations and their influence in the main clinical outcomes. NK cells were analyzed at the diagnosis in a central laboratory. Material and methods: We analyzed NK cell subpopulations based in the expression of DNAM-1, TIGIT, TACTILE, CD8, PD-1, TIM-3, LAG-3, NKp44, NKp46, NKp30, CD16, CD85j,KIR2D, NKG2C, NKG2A, CD57, CD6, CD244, NKp80, Perforin, Granulolysin and Granzyme B. We compare composite Complete Remission (CRc) results of the Venetoclax/Quizatinib with Aza or Cytarabine vs. not achieving CRc using t Student. MaxStat statistics was used to test the significant limit of those populations with a significant difference (R-statistics version 4.2.2). Survival analysis comparing significant differences between patients in CRc was performed using LogRank test and Kaplan Maier. Cox survival analysis was performed to evaluate if the presence of this populations could be an independent factor against the European Leukemia Net classification of 2017 and p53. Data of molecular characteristics were obtained with an NGS panel of 40 genes. RESULTS: The trial included 76 ineligible patients for intensive chemotherapy (37 and 39 were in Aza and LDAC arms respectively). cCR was obtained in 39 patients (51.3%). ELN2017 risk was favorable in 8, intermediate in 15, and Adverse in 53. In 70 patients NK cell populations were analyzed (4 patients with very low percentage of NK cells, 2 with no sample at diagnosis were excluded from the study). There were significant differences between patients who achieve CRc and those who did not, according to DNAM-1 (74.4% vs 61.9, p=0.0018) and TACTILE (62% vs. 72%, p=0.02) expression on NK cells. The rest of antigens analyzed on NK cells were not significant. We found a cutoff of 62% of DNAM-1+ and less than 81% of TACTILE to differentiate populations in terms of survival using long-rank test. The number of DNAM-1 positive was 47 (60%) and TACTILE- was 55 (78%). The median OS of DNAM-1+ was better than DNAM-1− (18.4 vs 4.7 months, p=0.0001), and between TACTILE− vs TACTILE+ (17,36 vs. 4.6 months, p=0.005). Using an Cox model comparing karyotype, p53 and DNAM-1+ and TACTILE-, only DNAM-1+ was associated with better outcome (HR:0.33 (0.17-0.66) and TACTILE+ with worse (HR: 2.44 (1.20-4.99) in multivariate analysis. Conclusions: DNAM-1(CD226) positive and TACTILE (CD96) negative NK cell populations are associated to CR and better OS. These findings need to be confirmed in larger studies. Interestingly, DNAM-1 is an activating receptor and TACTILE is an inhibitory receptor for NK cells that share the same CD155 ligand but display opposite function.

Preclinical Characterization of the Anti-Leukemia Activity of the CD33/CD16/NKG2D Immune Modulating TriNKET ® BMS-986357 (CC-96191)

CD33 is widely expressed by myeloid cells and is a validated drug target in acute myeloid leukemia (AML), as shown by the benefit of some patients from the CD33 antibody-drug conjugate gemtuzumab ozogamicin (GO). However, GO is often ineffective and toxic, prompting interest in more potent CD33-directed therapies. Success of T cell-engaging bispecific antibodies in lymphoid malignancies has raised enthusiasm for similar agents targeting CD33, but toxicities from activated T cells cause significant challenges for their use and provide a strong rationale to explore drugs engaging natural killer (NK) cells. Here, we investigated BMS-986357, a TriNKET ® that activates NK cells via CD16 and NKG2D receptors while targeting CD33. This format was chosen because simultaneous engagement of multiple activating NK cell receptors yields greater cytotoxic activity against neoplastic cells than engagement via a single activating receptor. Surface plasmon resonance analyses showed BMS-986357 simultaneously binds CD33, NKG2D, and CD16a, and co-engagement of NKG2D and CD16a increases the avidity. In the presence of primary human NK cells from healthy donors or a human NK cell line, the TriNKET ® demonstrated broad cytolytic anti-leukemia activity in a strictly CD33-dependent manner using a panel of CD33-expressing or CD33-deficient/deleted acute leukemia cells. Consistent with this, removing the CD33 binding domain rendered BMS-986357 ineffective against CD33+ AML cells. Drug-induced cytotoxicity was greater with BMS-986357 than with monoclonal CD33 antibodies, including lintuzumab and an afucosylated antibody with enhanced NK function, demonstrating the benefit of the TriNKET ® format. Compared to BMS-986357, substantially less cytotoxicity was observed with an Fc-mutant variant of BMS-986357 that abrogates binding to CD16a or an NKG2D dead-arm TriNKET ®, and cytolytic effects were reduced with a CD16-deficient NK cell line vs. a CD16-expressing subline, indicating maximal efficacy of BMS-986357 required co-engagement of CD16a and NKG2D. Using sublines of OCI-AML3 and KG-1 cells (both cell lines with low endogenous CD33 expression) to overexpress wild-type CD33 at increasing levels, we found low abundance of CD33 curtailed BMS-986357-induced cytotoxicity. Flow cytometric binding studies identified BMS-986357 to recognize the membrane-distal V-set domain of CD33. Unlike GO, BMS-986357-mediated cytolysis was not affected by over-expression of ABC transporter proteins by AML cells. The potency but not maximal activity of BMS-986357 was reduced by super-physiologic concentrations of soluble CD33; in contrast, the soluble form of the NKG2D ligand MICA did not impact TriNKET ® activity. In the presence of CD33+ AML cells, BMS-986357 activated NK cells but not T cells from healthy donor peripheral blood mononuclear cells and produced similar levels of maximum cytolysis as a CD33/CD3 bispecific antibody. Despite this, BMS-986357 elicited 10 to >100-fold lower soluble cytokine levels including IFN-γ, TNF, IL-6, and GM-CSF than a CD33/CD3 bispecific antibody, suggesting BMS-986357 has the potential for CD33/CD3 bispecific-like efficacy without the associated risk of cytokine release syndrome. Finally, in bone marrow specimens from patients with AML, BMS-986357 killed AML cells but not normal monocytes, suggesting selectivity of drug-induced cytotoxicity toward neoplastic cells, consistent with the notion NK cells are capable to differentiate between healthy and leukemic CD33+ cells. This selectivity suggests BMS-986357 may produce less myelosuppressive toxicity than what has been observed with CD33 targeting antibody-drug conjugates. In summary, our findings demonstrate that BMS-986357 TriNKET ® has potent CD33-dependent cytolytic activity in vitro against human AML cells, supporting the drug's exploration in early phase clinical trials. One such trial (NCT04789655) has opened accrual for adults with relapsed/refractory AML.

The KIR-HLA-CD16a Immunogenetic Profile Influences NK Cell-Mediated ADCC and Response to Rituximab Therapy in B-Cell Lymphomas

Rituximab-based chemoimmunotherapy (R-CHOP) is the standard of care in most B-cell lymphomas, however there is marked interpatient heterogeneity in treatment response. An important mechanism of Rituximab (anti-CD20) action is through natural killer (NK) cell-mediated antibody-dependent cellular cytotoxicity (ADCC), but the factors influencing this are poorly understood. Here, we present findings from a preclinical study investigating the role of NK cell receptor polymorphisms and HLA allelic variation on ADCC against aggressive B-cell lymphoma cell lines. Genotyping was conducted using Luminex-based SSO and Sanger sequencing. Multicolor flow cytometry was used to assess the response of activated NK cells from healthy donors against 8 lymphoma cell lines. Individuals carrying the GG or GT allele in CD16a were found to have a 3-8 fold greater NK cell response compared to individuals with a TT allele and rituximab-mediated ADCC was significantly greater in individuals with a KIR-3DL1 allele when tested against B-cell lymphomas lacking the HLA-Bw4 allele. An additive effect was observed when considering both CD16a and KIR-HLA together. As expected, CD20 expression was a strong correlate of NK cell response. In summary, NK cell-mediated ADCC in response to ADCC appears to be influenced by the KIR-HLA-CD16a genotype. These findings suggest a potential role for immunogenotyping in B-cell lymphomas treated with Rituximab. Additionally, the presence of the shared F c receptor domain opens the possibility of applying this framework towards predicting NK cell responses to antibody therapies in other diseases.

Chimeric Antigen Receptor-Engineered NK Cells Overcome CD226 Downregulation As an Immune Escape Mechanism in Acute Myeloid Leukemia

Background: Natural killer (NK) cells are part of the innate immune system, and their killing capacity depends on the inputs from activating and inhibitory receptors. CD226 is an activating receptor that plays a role in the immune surveillance of acute myeloid leukemia (AML). AML cells have developed mechanisms to escape NK cell cytotoxicity including downregulating activating receptors such as CD226 on the surface of NK cells. Chimeric antigen receptors (CARs) are synthetic receptors integrated into NK cells to direct their anti-leukemia activity, and CD38 is a potential target for NK CAR-based cellular therapy against AML. Understanding the dynamics between the endogenous activating and inhibitory NK cell receptors (such as CD226) and the introduced CAR can determine the development of more effective NK CAR-based therapy for AML. We hypothesize that CD38-directed CAR NK cells may overcome CD226 downregulation as a mechanism of immune escape in AML. Purpose: we aimed to investigate (1) the mechanisms developed by AML cells to escape recognition by the activating receptor CD226, (2) whether and how anti-CD38 CAR-armed NK cells can overcome AML immune escape mechanisms. Methods: we performed multiparametric mass spectrometry to characterize changes in CD226 expression in NK cells of individuals with AML. Then, we investigated CD226 expression in NK cell-AML cocultures to characterize CD226-related mechanisms by imaging flow cytometry. Finally, to explore the impact of CD226 knockout (KO) together with the role of CD38 CAR in NK cell functionality, we retrovirally transduced CD38 CAR combined with CRISPR-Cas9 CD226 KO followed by short- and long-term cytotoxicity assays, cytokine production techniques and immune synapse assays by imaging flow cytometry. Results: NK cells from AML patients expressed low levels of CD226 with impaired cytotoxicity compared to heathy donor NK cells. Co-culture of healthy donor NK cells with AML blasts resulted in CD226 downregulation secondary to its internalization and was dependent on expression of the CD226 ligand CD155 in AML cells. CD226 KO diminished NK cell cytokine production and decreased their killing capacity against AML cells. In contrast, CD38-targeting NK cells displayed enhanced and specific cytotoxic activity against primary AML cells. When we combined the CD38 CAR with a CD226 KO in NK cells, these cells maintained their activating potential, cytokine secretion levels, and anti-leukemic cytotoxicity (Figure 1). CD38 CAR / CD226 KO NK cells could build strong immune synapses (Figure 2) even in the absence of LFA-1, an integrin activated by CD226 signaling and essential for NK cell immune synapse formation, suggesting that the CAR molecule compensates for the absence of CD266-mediated LFA signaling. Furthermore, CD38 CAR NK cells were capable of forming immune synapses, that were at least partially independent from LFA-1. Conclusion: CAR-directed NK cells can surpass resistance mechanisms in AML, such as CD226 downregulation and dampening of LFA-1 recruitment into the immunological synapse. Thus, NK cell activation by artificially introduced and germline-encoded receptors can overcome distinct tumor-resistance mechanisms, CAR-driven NK cells being a potent option for the treatment of AML.

Selinexor Enhances Natural Killer Cell Function Against Multiple Myeloma Cells

Introduction: Natural killer (NK) cells are innate immune effector cells which can mediate antibody dependent cellular cytotoxicity (ADCC) and lyse cancer cells. Harnessing NK cell function against multiple myeloma (MM) is of high interest and multiple strategies are currently under development. Exportin-1 (XPO1) is a nuclear export protein which inhibits the function of tumour suppressor proteins and facilitates oncogene mRNA translation. Selinexor is a first-in-class XPO1 inhibitor approved for the treatment of relapsed or refractory MM that induces cancer cell apoptosis. In addition, selinexor has recently been shown to promote NK cell cytotoxicity against B cell lymphoma cells. This study aimed to determine whether selinexor augments NK cell activation against MM cells both alone, and in combination with the anti-CD38 antibody daratumumab. Methods: A panel of MM cell lines (MM.1S, U266 and RPMI-8226) were incubated with clinically relevant concentrations of selinexor for 24 hours, then either assessed for expression of ligands for NK cell receptors (KIR, NKG2A, NKG2D and NKp46), or co-cultured with primary human NK cells ± daratumumab. Following co-culture, NK-mediated lysis of MM cells was assessed by propidium iodide staining and NK cell degranulation assessed by CD107a expression. Results: Selinexor pre-treatment of MM cells significantly increased NK cell degranulation (p<0.05) and enhanced NK specific lysis of MM targets (p<0.05). Furthermore, selinexor pre-treatment significantly (p<0.05) enhanced NK cell activation in combination with daratumumab compared to daratumumab alone. Importantly, selinexor did not alter surface expression of CD38 on MM cell lines. To investigate the mechanism behind this enhanced NK cell function, we assessed the effect of selinexor on the expression of NK cell ligands by MM cells. Selinexor increased the expression of ULBP1/2/5/6 (2-fold, p<0.001) which bind to the NK cell activating receptor NKG2D. In addition, selinexor decreased MM cell expression of HLA-E (30% decrease, p<0.05) which binds to the inhibitory NK receptor NKG2A. Conclusions: These data suggest that selinexor may promote the efficacy of NK targeted therapeutics in multiple myeloma.

The NK Cell Receptor NKp46 Acts As an Essential Regulator of ILC1 Proliferation, Effector Function and Anti-AML Activity

Innate lymphoid cells (ILCs) are tissue-resident innate immune cells that respond rapidly to infection and secrete inflammatory mediators. Group 1 includes ILC1s and NK cells. Both cell types produce IFN-γ and require T-BET for their function; however, at least in mice, ILC1s do not express EOMES while NK cells do. The NKp46 receptor, encoded by the Ncr1 gene, plays an important role in NK cells. Non-NK immune cells, including ILC1s also express NKp46. However, the role of NKp46 in these non-NK immune cells remains largely unknown. We previously reported that NKp46 deficiency reduces both the percentages and numbers of ILC1s in mice but not the proportions of NK cells, ILC2s, and ILC3s (Wang et al., Plos Biology, 2018), suggesting that NKp46 may play a unique role in ILC1s. However, the precise mechanism by which NKp46 regulates ILC1s is yet to be determined. Using RNA-seq, we identified 35 upregulated genes and 66 downregulated genes in mutant ILC1s ( Ncr1 gfp/gfp) compared to wild-type ( Ncr1 +/+)ILC1s ( p < 0.05). Among the genes that were differentially expressed, we noted decreased expression of the cytokine receptors Il-18r1, Il-7rα, and Il-2rα in Ncr1 gfp/gfpILC1s compared to Ncr1 +/+ILC1s. Using gene set enrichment analysis of RNA-seq data from freshly sorted ILC1s from the livers of Ncr1 +/+and Ncr1 gfp/gfpmice, we identified the top 10 pathways associated with downregulated genes. Notably, NKp46 deletion significantly affected NF-κB. We validated this finding by treating ILC1s with NKp46 antibody and found that the phosphorylation of NF-κB p65 subunit was increased. The downregulation of IL-2Rα and IL-7Rα on Ncr1 gfp/gfpILC1s led us to investigate whether NKp46 also regulates ILC1 proliferation, survival, or persistence. We observed comparable levels of apoptosis in ILC1s freshly isolated from Ncr1 +/+and Ncr1 gfp/gfpmice. Thus, lack of NKp46 does not affect ILC1 apoptosis. However, expression of the proliferation marker Ki67 was significantly downregulated in freshly isolated Ncr1 gfp/gfpILC1s compared to Ncr1 +/+ILC1s. We also intravenously ( i.v.) co-transferred equal numbers of FACS-sorted Ncr1 +/+ and Ncr1 gfp/gfpILC1s labeled with CellTrace™ Violet dye (to distinguish donor cells from host cells) into immunodeficient recipient Rag2 −/− Il2γc −/− mice. After one week, the population of Ncr1 gfp/gfpILC1s was less than those of Ncr1 +/+ILC1s in the recipient Rag2 −/− Il2γc −/− mice ( p = 0.0002, n = 5), indicating that ILC1 proliferation requires NKp46 in vivo. To investigate the functional relevance ofNKp46, we i.v. injected C1498 AML cells into Ncr1 +/+or Ncr1 gfp/gfpmice. The Ncr1 gfp/gfpmice exhibited significantly more tumor growth than the Ncr1 +/+mice. Animal survival was significantly shorter in the Ncr1 gfp/gfpmice compared to Ncr1 +/+mice ( p = 0.0023, n > 9). Injection of additional Ncr1 +/+ILC1s into Ncr1 +/+mice increased survival compared to animals without additional Ncr1 +/+ILC1 administration ( p = 0.0183, n = 6). Further, this injection managed to rescue the dramatic decrease in the number of ILC1s observed in the Ncr1 gfp/gfpmice. This increased survival was in stark contrast to the Ncr1 gfp/gfpmice without Ncr1 +/+ILC1 injection, or those who received Ncr1 gfp/gfpILC1 injection. We also investigated the role of NKp46 in human ILC1s. Human ILC1s isolated from peripheral blood mononuclear cells (PBMCs) were treated with a human NKp46 antibody, increasing Ki67 expression. Next, we sorted NKp46 - and NKp46 + ILC1s from human PBMCs and co-cultured them with MOLM13 AML cells for 24 h and found the human NKp46 - ILC1s were significantly less cytotoxic compared to NKp46 + ILC1s. In conclusion, NKp46 is indispensable for ILC1 expression of IL-2Rα. Deficiency of NKp46 in mice reduces IL-2Rα expression on ILC1s by downregulating NF-κB signaling, thus impairing ILC1 proliferation. In a mouse model of AML, we see the functional consequences of cellular impairment as NKp46 deficiency eliminates the ability to control tumor growth and reduces survival. These changes can be reversed by injection of sufficient numbers of NKp46 + ILC1s into mice deficient for the receptor. Human NKp46 + ILC1s also exhibit stronger cytokine production and cytotoxicity than their NKp46 -counterparts, suggesting that NKp46 plays a similar role in both humans and mice. Our findings suggest a novel strategy for activating NKp46 signaling to promote ILC1 proliferation and anti-tumor activity.

Post-Transplant Nivolumab Plus Unselected Autologous Lymphocytes in Truly Refractory Hodgkin Lymphoma Patients Is Highly Effective and Responses Are Mediated By NK Cells

Background In the relapsed/refractory Hodgkin Lymphoma (HL) setting (RHL), the achievement of complete remission (CR) is fundamental in order to proceed with allogeneic stem cell transplantation (HSCT) consolidation. Immune checkpoint inhibitors (CI) have demonstrated clinical activity in patients relapsing after ASCT, although only 20% CR rate is observed. In order to improve the efficacy of CI in RHL, we previously reported a salvage treatment based on early CI therapy following post-autologous stem cell transplantation (ASCT) with the reinfusion of unselected autologous lymphocytes infusions (ALI). The rationale of this approach is based on the achievement of a disease debulking through ASCT conditioning. Early administration of CI (nivolumab) is performed on a minimal disease burden, while reinfusions of ALI reduce post ASCT immune depression eliciting CI efficacy. Aims The aim of this study was to evaluate the efficacy of the procedure in terms of CR rates and overall survival (OS) after an extended follow up. Biological endpoint was to investigate the lymphocyte subpopulations involved in the mechanism of response and investigate the role of NK-cells mediating anti tumor responses in HL. Methods Patient were eligible to this study after failure to respond to first line treatment (i.e. positive PET2 or PET6 scan) and underwent autologous lymphocyte apheresis upon enrollment. All patients received conventional 2nd line chemo followed by 3rd line chemo-immunotherapy with Brentuximab-Vedotin (BV) in non-responding patients. Patient failing to achieve CR after BV were enrolled in the treatment arm and proceeded to ASCT + CI and ALI, whereas patients responding to 2nd- or 3rd treatment received ASCT followed by ALI alone, as a control cohort (figure 1A). NK cell degranulation assay was evaluated by staining for CD107a (LAMP-1) expression on healthy-donors derived NK cells exposed to HL cell lines (L428 and L250), in the presence or absence of monoclonal antibodies targeting inhibitory or activating receptors. Surface and intracellular staining was performed prior to flow cytometry and analysis was performed on the CD3-/CD56+ gated population. Results Twenty-one patients with RHL (median age 32 years; range 18-65) underwent lymphocyte apheresis after failure of 1st line chemo and then proceeded to salvage therapy. Thirteen patients failed to respond to 2nd and 3rd line therapy and thus received early post-transplant CI supported with four ALI. Eight patients responded to 2nd line chemo (n=6) or 3rd line BV (n=2) and received ASCT followed by ALI alone. No adverse events were recorded, specifically, no immune-related toxicity was observed. All patients receiving ALI + CI (treated patients) achieved negative PET scan CR. Eight of them received HSCT consolidation. One patient refusing HSCT after achieving CR in this study relapsed and responded to CI re treatment followed by HSCT. All patients in the treatment arm are alive and disease-free after a median follow-up of 32 months (95% CI 26.4-51.0). Median disease-free survival (DFS) was not reached in treatment arm (Fig 1B). Four of the patients in the control arm relapsed (50%). Three of them responded to 3rd line therapy and proceeded to HSCT. One patient achieved CR with conventional CI treatment but refused HSCT and the other relapsing patient died because of progressive lymphoma after failure to achieve CR with conventional single agent CI. Median DFS in the control arm was 22 months (Fig 1B). NK cells showed higher expansion and a faster maturation in the treatment arm, compared to the control arm (p<0.05). As expected, HL cells lines do not express HLA class I and II, but express activating NK cells receptors (aNKG2D, aNKp30, aNKp46, aDNAM-1). In vitro, the activation of each of those receptors was able to trigger NK cells degranulation. Similarly, PD-L1 and PD-L2 blockade on HL cell lines significantly increased NK cell degranulation (p<0.05). Taken together, those observations support the role of NK cells in this setting. Conclusions Our data show very high anti-tumor activity of ALI + CI for RHL, allowing most patients to proceed to HSCT. RHL patients in the treatment arm had an excellent outcome if compared to the control arm, which included patient who did respond to conventional treatment. Biological data suggests that this approach may accelerate NK cell development/maturation and suggest that NK cells may mediate response to CI in HL.

NK Cell Dysfunction in CLL Is Mediated through SHP-1 Signaling and Is Associated with Poor Prognosis

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, presenting with a highly variable clinical course, outcome and response to therapy. This variability has been linked to a complex tumor microenvironment and genetic/epigenetic modifications that lead to immunosuppression. Indeed, the clinical hallmark of this disease is the susceptibility to infections and secondary malignancies. While T cell dysfunction in CLL has been well described, conflicting information exists on NK cell changes in CLL and their role in CLL immunosurveillance. Here, we analyzed samples from 75 untreated (or completed treatment >2 years ago) CLL patients and 30 healthy controls. We discovered a substantial variation in NK cell function compared with healthy controls, which we further classified into hyperfunctional, normofunctional and dysfunctional based on their ability to degranulate, and produce IFN- γ in response to K562 targets ( Figure 1). NK cells from ‘dysfunctional’ CLL samples also displayed impaired cytotoxicity against K562 targets, weaker synapse formation and Syk/Zap70 signaling in response to antibody-dependent cellular cytotoxicity (ADCC) compared to those from ‘functional’ samples. The NK functional status was strongly associated with multiple prognostic markers, including cytogenetics, IgVH mutation status, ZAP-70 expression and disease stage, with patients with dysfunctional NK cells having significantly higher rates of secondary malignancies and viral infections ( Table 1). Using multispectral flow cytometry we discovered high phenotypic heterogeneity with unique NK cell clusters present in the dysfunctional samples. Those clusters express a pattern of activation-induced exhaustion, with upregulation of multiple checkpoint molecules such as PD-1, TIGIT, LAG-3, KLRG-1, TIM-3 but not evidence of terminal differentiation (CD57 negative). Those clusters also showed concomitant expression of activating molecules such as NKG2D and DNAM-1, suggesting reversibility of their dysfunctional status. We subsequently found significantly higher (p<0.0001) constitutive phosphorylation of SHP-1 protein, a phosphatase downstream of multiple inhibitory NK cell receptors, in NK cells from dysfunctional samples. Treatment with a SHP-1 inhibitor NSC-87877 (EMD Millipore) or use of siRNA targeting SHP-1 (ThermoFisher scientific), resulted in reversal of NK dysfunction with full restoration of their functional capacity. Taken together, our data suggest that NK cells functional status plays an important role in CLL disease progression and secondary complications. The novel mechanism of NK cell immune dysfunction in CLL described here has the potential to improve outcomes with novel immunotherapies such as chimeric antigen receptors, checkpoint inhibitors and bi-specific antibody therapy that have shown disappointing results in CLL to date when compared with other B cell malignancies.

Anti-TIM3 chimeric antigen receptor-natural killer cells from engineered induced pluripotent stem cells effectively target acute myeloid leukemia cells

BackgroundAcute myeloid leukemia (AML) is a clonal malignant disorder which originates from a small number of leukemia-initiating cells or leukemic stem cells (LSCs)—the subpopulation that is also the root cause of relapsed/refractory AML. Chimeric antigen receptor (CAR)-T cell therapy has proved successful at combating certain hematologic malignancies, but has several hurdles that limit its widespread applications. CAR-natural killer (NK) cells do not carry the risk of inducing graft-versus-host disease (GvHD) frequently associated with allogeneic T cells, thereby overcoming time-consuming, autologous cell manufacturing, and have relatively safer clinical profiles than CAR-T cells. The present study aimed to generate anti-TIM3 CAR-NK cells targeting LSCs from a clonal master induced pluripotent stem cells engineered with the third-generation anti-TIM3 CAR.MethodsA clonal master umbilical cord blood NK-derived induced pluripotent stem cell (iPSC) line, MUSIi013-A, was used as a starting cells for engineering of an anti-TIM3 CAR harboring TIM3 scFv fragment (clone TSR-022), CD28, 4-1BB, and CD3ζ signaling (CAR-TIM3). The established CAR-TIM3 iPSCs were further differentiated under serum- and feeder-free conditions into functional CAR-TIM3 NK cells and tested for its anti-tumor activity against various TIM3-positive AML cells.ResultsWe successfully established a single-cell clone of CAR-TIM3 iPSCs, as validated by genomic DNA sequencing as well as antibody and antigen-specific detection. We performed thorough iPSC characterization to confirm its retained pluripotency and differentiation capacity. The established CAR-TIM3 iPSCs can be differentiated into CAR-TIM3 NK-like cells, which were further proven to have enhanced anti-tumor activity against TIM3-positive AML cells with minimal effect on TIM3-negative cells when compared with wild-type (WT) NK-like cells from parental iPSCs.ConclusionsiPSCs engineered with CARs, including the established single-cell clone CAR-TIM3 iPSCs herein, are potential alternative cell source for generating off-the-shelf CAR-NK cells as well as other CAR-immune cells. The feasibility of differentiation of functional CAR-TIM3 NK cells under serum- and feeder-free conditions support that Good Manufacturing Practice (GMP)-compliant protocols can be further established for future clinical applications.

Potentiation of natural killer cells to overcome cancer resistance to NK cell-based therapy and to enhance antibody-based immunotherapy.

Natural killer (NK) cells are cellular components of the innate immune system that can recognize and suppress the proliferation of cancer cells. NK cells can eliminate cancer cells through direct lysis, by secreting perforin and granzymes, or through antibody-dependent cell-mediated cytotoxicity (ADCC). ADCC involves the binding of the Fc gamma receptor IIIa (CD16), present on NK cells, to the constant region of an antibody already bound to cancer cells. Cancer cells use several mechanisms to evade antitumor activity of NK cells, including the accumulation of inhibitory cytokines, recruitment and expansion of immune suppressor cells such as myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs), modulation of ligands for NK cells receptors. Several strategies have been developed to enhance the antitumor activity of NK cells with the goal of overcoming cancer cells resistance to NK cells. The three main strategies to engineer and boost NK cells cytotoxicity include boosting NK cells with modulatory cytokines, adoptive NK cell therapy, and the employment of engineered NK cells to enhance antibody-based immunotherapy. Although the first two strategies improved the efficacy of NK cell-based therapy, there are still some limitations, including immune-related adverse events, induction of immune-suppressive cells and further cancer resistance to NK cell killing. One strategy to overcome these issues is the combination of monoclonal antibodies (mAbs) that mediate ADCC and engineered NK cells with potentiated anti-cancer activity. The advantage of using mAbs with ADCC activity is that they can activate NK cells, but also favor the accumulation of immune effector cells to the tumor microenvironment (TME). Several clinical trials reported that combining engineered NK cells with mAbs with ADCC activity can result in a superior clinical response compared to mAbs alone. Next generation of clinical trials, employing engineered NK cells with mAbs with higher affinity for CD16 expressed on NK cells, will provide more effective and higher-quality treatments to cancer patients.

Application of chimeric antigen receptor-natural killer cells for the treatment of type 1 diabetes

For the past 100 years, insulin supplementation has been the mainstay of treatment for type 1 diabetes (T1D), which is characterized by progressive autoimmune-mediated loss of insulin-producing β cells in the islets of Langerhans over the last decades, technological advances in glucose monitoring and therapeutics have greatly improved the care and management of these patients. However, morbidity, mortality, and quality of life remain challenges for patients with T1D. Islet transplantation has been successfully performed, but there are several limiting factors, such as the lack of cadaveric donors and the need for lifelong immunosuppressive therapy. Therefore, there is a great medical need for alternative therapeutic approaches. In the current review, the current knowledge on novel approaches for the treatment of T1D with a focus on the potential of using chimeric antigen receptor (CAR)-T cells and natural killer (NK) cells is summarized.

Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection.

The SARS-CoV-2 pandemic has affected nations globally leading to illness, death, and economic downturn. Why disease severity, ranging from no symptoms to the requirement for extracorporeal membrane oxygenation, varies between patients is still incompletely understood. Consequently, we aimed at understanding the impact of genetic factors on disease severity in infection with SARS-CoV-2. Here, we provide data on demographics, ABO blood group, human leukocyte antigen (HLA) type, as well as next-generation sequencing data of genes in the natural killer cell receptor family, the renin-angiotensin-aldosterone and kallikrein-kinin systems and others in 159 patients with SARS-CoV-2 infection, stratified into seven categories of disease severity. We provide single-nucleotide polymorphism (SNP) data on the patients and a protein structural analysis as a case study on a SNP in the SIGLEC7 gene, which was significantly associated with the clinical score. Our data represent a resource for correlation analyses involving genetic factors and disease severity and may help predict outcomes in infections with future SARS-CoV-2 variants and aid vaccine adaptation.

Transcriptomic Analysis of Clonal Hematopoiesis in Solid Tumors Reveals Driver Mutation-Specific Patterns of Immune Dysregulation

Introduction: Clonal hematopoiesis (CH) is a pre-malignant state wherein somatic mutations confer a proliferative advantage to hematopoietic stem cells, driving inflammatory changes that increase the risk of age-related diseases and mortality. CH is common in individuals with solid cancers and associated with poorer overall survival due to increased tumor progression, raising the possibility that CH alters the tumor-immune microenvironment (TIME). This study defines the inflammatory program of tumor-infiltrating leukocytes to help elucidate the role of CH in the TIME. Methods: Somatic mutations compatible with CH were detected in the whole exome sequences of 6,537 cancer patients with 16 major cancer types from The Cancer Genome Atlas (TCGA) project using Mutect2. CH variant curation followed a pre-defined list of putative variants in 63 genes known to drive hematologic clonality. Calls were filtered to remove sequencing artifacts, germline variants, and small clones with variant allele fraction (VAF) < 2%. Bulk RNA-seq analysis was conducted on data from the colon adenocarcinoma (n=240) and lung adenocarcinoma (n=402) groups. Sequencing reads were pseudo-aligned and quantified with kallisto, then differential expression analysis was performed with DESeq2, controlled for cancer type, tumor biopsy site, and patient sex. Differentially expressed genes were subject to gene set enrichment analysis (GSEA) of gene ontology (GO) terms using clusterProfiler. Results: The prevalence of CH in this cohort was 8.8% (n=576/6,537) and its presence was strongly associated with age (p=1.0x10 -25). The highest rate of CH was found in cutaneous melanoma (23.5%, n=110/468) and the lowest rate was in esophageal carcinoma (2.4%, n=3/126). Most patients with CH had just 1 variant (82.8%, n=477/576), but some patients exhibited 2 variants (10.1%, n=58/576), and a small group of patients carried 3 or more variants. A total of 772 CH variants were detected in the cohort, and as expected their distribution across the CH driver genes was not uniform: DNMT3A mutations were most common (n=193), followed by TET2 (n=59), and ASXL1 (n=47; Fig 1). KMT2C mutations were also present in this cohort (n=41) at far higher rates than reported in the general population, providing possible evidence that KMT2C-mutant CH is associated with cancer or its treatments. Across the group of colon and lung cancer patients subject to RNA-seq analysis, a total of 220 genes (111 upregulated, 109 downregulated) were found to be differentially expressed by CH status at p adj < 0.05. GSEA of GO terms revealed significant activation of gene sets involved in innate and adaptive immune processes with upregulation of both positive and negative regulatory systems, suggesting more intricate mechanisms of immune dysfunction as opposed to generalized hyper-inflammatory activity in the TIME (Fig. 2). GSEA also revealed enrichment of non-immune pathways tied to tumorigenesis. Among the significantly dysregulated genes are the neutrophil activators PPBP and CXCL6, monocyte/macrophage markers LILRA2, CPM, CHI3L1, and CD163L1, and the natural killer cell receptors KLRC2/3. Strikingly, these inflammatory changes were absent in patients with DNMT3A, TET2, or ASXL1 (DTA) CH, and were instead driven by non-DTA CH mutations in a VAF-dependent manner. Investigation of tumor transcriptomes within each cancer type revealed that CH in colon cancer patients has reciprocal effects on inflammation and immunity - DTA CH in this cancer demonstrated suppression of immune-associated gene sets while non-DTA CH was more consistent with the general trend of immune enrichment and activation. Conclusions: This work demonstrates that while general inflammatory changes are evident at the tumor level with CH, there is a critical need to recognize the nuances of CH-associated immune mechanisms in cancer, which appear to vary by cancer type and CH driver. Ongoing efforts will continue to characterize the TIME of the other TCGA cancers through transcriptomic analysis and in situ histological imaging. This study also provides some early clinical evidence for the selection of KMT2C variants in cancer patients, though more work is needed to understand their clonal dynamics and clinical implications. In light of these findings, future studies will pave the way for CH as a biomarker in cancer medicine and a cornerstone of precision immuno-oncology.

Targeted Integration of a Chimeric Antigen Receptor in Key Selected Loci in Primary Natural Killer Cells

Despite promising preclinical studies and early clinical data (Liu et al., NEJM, 2020), chimeric antigen receptor natural killer cells (CAR NK) are not yet on par with CAR T cells for the treatment of malignant diseases. Much effort has gone into developing NK-optimized CAR architectures (Li et al., Cell Stem Cell, 2018) and to increasing the persistence of CAR NK cells. We hypothesized that CAR NK cells could also benefit from the targeted integration of a CAR transgene, as compared with semi-random integration obtained using gammaretroviral vectors. Precise targeting has proven highly advantageous for TRAC CAR T cells owing to the optimal regulation and homogeneous expression conferred by the endogenous TCR alpha promoter (Eyquem et al., Nature, 2017). We first optimized an editing protocol for primary NK cells that uses electroporation of a CRISPR/Cas9 ribonucleoprotein followed by transduction with AAV6 bearing a homology-directed repair template. With this protocol we were able to knock out (KO) genes (including CD38, B2M, and different NK receptors), knock in transgenes (GFP-fusion protein, truncated EGFR, CAR), or both, at high efficiency. There was only moderate cell toxicity, and proliferation and cytotoxicity were conserved. Because of the high constitutive expression of B2M, we initially chose to focus on this locus and targeted a 1928z CAR transgene for regulation under the endogenous B2M promoter; our template design also rescues the B2M gene upon knock-in, enabling intermediate B2M expression (Figure 1). This strategy conferred high expression of the CAR and significantly more homogeneity as compared with gammaretroviral delivery (Figure 1). Furthermore, the rescued B2M expression protected B2M CAR NK cells from fratricide killing, whereas the B2M KO NK cells and the CAR NK cells with disrupted B2M expression were susceptible. B2M CAR NK cells also displayed higher in vitro cytotoxicity as compared with WT NK cells against two different CD19-expressing tumor cell lines (NALM6, SupB15). We tested B2M CAR NK cells in an NSG mouse xenograft model with an intraperitoneally injected human ovarian cancer cell line engineered to express CD19 (CD19 + SKOV3). Unexpectedly, compared to retroviral CAR-NK cells, B2M CAR NK cells conferred less tumor control (assessed by bioluminescence imaging) and less of a survival benefit. Therefore, we screened a panel of other loci for CAR targeting: five for NK activating receptors ( CD16A, CD56, DNAM1, NKp30, NKp46) and four for NK inhibitory receptors ( CD161, LILRB1, NKG2A, TIGIT). For activating receptors, the transgene was designed to use the endogenous promoter and to maintain expression of the targeted locus. For inhibitory receptors, the transgene was placed under the control of an EF1a exogenous promoter and designed to disrupt expression of the targeted locus. We compared these constructs and the initial B2M CAR NK design for CAR expression (by flow cytometry) and in vitro functionality (cytotoxicity assays) and observed wide variation in knock-in efficiency and CAR expression (Figure 2). For the top constructs based on knock-in efficiency, we conducted in vitro cytotoxicity assays against NALM6 and SupB15 cell lines. We found that when normalized for CAR percentage using the respective KO conditions, all tested knock-in loci performed better than B2M CAR NK cells, despite the lower CAR expression. Our current focus is on validating these top loci for the targeted integration of a 1928z CAR using in vivo models for comparison with B2M CAR NK and retroviral CAR NK. In summary, we have identified advantageous in vitro characteristics for the targeted integration of a CAR transgene in primary NK cells and screened 10 loci for CAR expression and in vitro cytotoxicity against tumor target cells. Confirmatory in vivo studies are ongoing and will be presented.