scholarly journals Single-Cell Sequencing Reveals the Novel Role of Ezh2 in NK Cell Maturation and Function

2021 ◽  
Vol 12 ◽  
Author(s):  
Minghang Yu ◽  
Ziyang Su ◽  
Xuefeng Huang ◽  
Xi Wang

Natural killer (NK) cells are lymphocytes primarily involved in innate immunity and exhibit important functional properties in antimicrobial and antitumoral responses. Our previous work indicated that the enhancer of zeste homolog 2 (Ezh2) is a negative regulator of early NK cell differentiation and function through trimethylation of histone H3 lysine 27 (H3K27me3). Here, we deleted Ezh2 from immature NK cells and downstream progeny to explore its role in NK cell maturation by single-cell RNA sequencing (scRNA-seq). We identified six distinct NK stages based on the transcriptional signature during NK cell maturation. Conditional deletion of Ezh2 in NK cells resulted in a maturation trajectory toward NK cell arrest in CD11b SP stage 5, which was clustered with genes related to the activating function of NK cells. Mechanistically, we speculated that Ezh2 plays a critical role in NK development by activating AP-1 family gene expression independent of PRC2 function. Our results implied a novel role for the Ezh2-AP-1-Klrg1 axis in altering the NK cell maturation trajectory and NK cell-mediated cytotoxicity.

2021 ◽  
Vol 218 (9) ◽  
Author(s):  
Siyu Tan ◽  
Xiaowei Guo ◽  
Mengzhen Li ◽  
Tixiao Wang ◽  
Zehua Wang ◽  
...  

The maturation and functional competence of natural killer (NK) cells is a tightly controlled process that relies on transcription factors (TFs). Here, we identify transcriptional repressor zinc fingers and homeoboxes 2 (Zhx2) as a novel regulator that restricts NK cell maturation and function. Mice with Zhx2 conditional deletion in NK cells (Zhx2Δ/Δ) showed accumulation of matured NK cells. Loss of Zhx2 enhanced NK cell survival and NK cell response to IL-15. Transcriptomic analysis revealed Zeb2, a key TF in NK cell terminal maturation, as a direct downstream target of Zhx2. Therapeutically, transfer of Zhx2-deficient NK cells resulted in inhibition of tumor growth and metastasis in different murine models. Our findings collectively unmask a previously unrecognized role of Zhx2 as a novel negative regulator in NK cell maturation and highlight its therapeutic potential as a promising strategy to enhance NK cell–mediated tumor surveillance.


2021 ◽  
Vol 6 (57) ◽  
pp. eabc9801
Author(s):  
Tim D. Holmes ◽  
Ram Vinay Pandey ◽  
Eric Y. Helm ◽  
Heinrich Schlums ◽  
Hongya Han ◽  
...  

Epigenetic landscapes can provide insight into regulation of gene expression and cellular diversity. Here, we examined the transcriptional and epigenetic profiles of seven human blood natural killer (NK) cell populations, including adaptive NK cells. The BCL11B gene, encoding a transcription factor (TF) essential for T cell development and function, was the most extensively regulated, with expression increasing throughout NK cell differentiation. Several Bcl11b-regulated genes associated with T cell signaling were specifically expressed in adaptive NK cell subsets. Regulatory networks revealed reciprocal regulation at distinct stages of NK cell differentiation, with Bcl11b repressing RUNX2 and ZBTB16 in canonical and adaptive NK cells, respectively. A critical role for Bcl11b in driving NK cell differentiation was corroborated in BCL11B-mutated patients and by ectopic Bcl11b expression. Moreover, Bcl11b was required for adaptive NK cell responses in a murine cytomegalovirus model, supporting expansion of these cells. Together, we define the TF regulatory circuitry of human NK cells and uncover a critical role for Bcl11b in promoting NK cell differentiation and function.


2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Kiekens ◽  
Wouter Van Loocke ◽  
Sylvie Taveirne ◽  
Sigrid Wahlen ◽  
Eva Persyn ◽  
...  

T-bet and Eomes are transcription factors that are known to be important in maturation and function of murine natural killer (NK) cells. Reduced T-BET and EOMES expression results in dysfunctional NK cells and failure to control tumor growth. In contrast to mice, the current knowledge on the role of T-BET and EOMES in human NK cells is rudimentary. Here, we ectopically expressed either T-BET or EOMES in human hematopoietic progenitor cells. Combined transcriptome, chromatin accessibility and protein expression analyses revealed that T-BET or EOMES epigenetically represses hematopoietic stem cell quiescence and non-NK lineage differentiation genes, while activating an NK cell-specific transcriptome and thereby drastically accelerating NK cell differentiation. In this model, the effects of T-BET and EOMES are largely overlapping, yet EOMES shows a superior role in early NK cell maturation and induces faster NK receptor and enhanced CD16 expression. T-BET particularly controls transcription of terminal maturation markers and epigenetically controls strong induction of KIR expression. Finally, NK cells generated upon T-BET or EOMES overexpression display improved functionality, including increased IFN-γ production and killing, and especially EOMES overexpression NK cells have enhanced antibody-dependent cellular cytotoxicity. Our findings reveal novel insights on the regulatory role of T-BET and EOMES in human NK cell maturation and function, which is essential to further understand human NK cell biology and to optimize adoptive NK cell therapies.


Blood ◽  
2010 ◽  
Vol 116 (8) ◽  
pp. 1308-1316 ◽  
Author(s):  
Nupur Bhatnagar ◽  
Henoch S. Hong ◽  
Jayendra K. Krishnaswamy ◽  
Arash Haghikia ◽  
Georg M. Behrens ◽  
...  

Abstract Natural killer (NK) cells and polymorphonuclear cells (PMNs) play a critical role in the first line of defense against microorganisms. Upon host infection, PMNs phagocytose invading pathogens with subsequent killing by oxidative or nonoxidative mechanisms. NK cells are known to have immunoregulatory effects on T cells, B cells, dendritic cells (DCs), and monocytes through secretion of various soluble products and cell-cell contact. However, their impact on PMN survival and function is not well known. We found that soluble factors derived from cytokine-activated NK cells delay PMN apoptosis and preserve their ability to perform phagocytosis and produce reactive oxygen species (ROS). The expression patterns of CD11b and CD62L on PMNs differed according to the cytokine combination used for NK-cell stimulation. Irrespective of the NK-cell treatment, however, PMN survival was prolonged with sustained functional capacity. We found that interferon γ, granulocyte-macrophage colony-stimulating factor, and tumor necrosis factor α produced by NK cells upon stimulation with cytokines played a crucial role in NK cell–mediated effects on PMNs. Our study demonstrates that soluble factors derived from cytokine-activated NK cells send survival signals to PMNs, which would promote their accumulation and function at the site of inflammation in vivo.


2021 ◽  
Vol 207 (6) ◽  
pp. 1555-1565
Author(s):  
Zhenlong Li ◽  
Yaoxin Gao ◽  
Cong He ◽  
Huan Wei ◽  
Jiang Zhang ◽  
...  

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Chao Yang ◽  
Jason R Siebert ◽  
Robert Burns ◽  
Yongwei Zheng ◽  
Ao Mei ◽  
...  

The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based on transcriptome, we identified five distinct NK cell clusters and define their relative developmental maturity in the bone marrow. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. Since mTORC2 regulates the expression of T-bet through AktS473-FoxO1 axis, we further characterized the T-bet-deficient NK cells and found an augmented immature transcriptomic signature. Moreover, deletion of Foxo1 restores the expression of T-bet and corrects the abnormal expression of immature NK genes. Collectively, our study reveals a novel role for mTORC2-AktS473-FoxO1-T-bet axis in suppressing the transcriptional signature of immature NK cells.


2021 ◽  
Vol 12 ◽  
Author(s):  
Eleonora Russo ◽  
Mattia Laffranchi ◽  
Luana Tomaipitinca ◽  
Annalisa Del Prete ◽  
Angela Santoni ◽  
...  

NK cells are innate lymphoid cells endowed with cytotoxic capacity that play key roles in the immune surveillance of tumors. Increasing evidence indicates that NK cell anti-tumor response is shaped by bidirectional interactions with myeloid cell subsets such as dendritic cells (DCs) and macrophages. DC-NK cell crosstalk in the tumor microenvironment (TME) strongly impacts on the overall NK cell anti-tumor response as DCs can affect NK cell survival and optimal activation while, in turn, NK cells can stimulate DCs survival, maturation and tumor infiltration through the release of soluble factors. Similarly, macrophages can either shape NK cell differentiation and function by expressing activating receptor ligands and/or cytokines, or they can contribute to the establishment of an immune-suppressive microenvironment through the expression and secretion of molecules that ultimately lead to NK cell inhibition. Consequently, the exploitation of NK cell interaction with DCs or macrophages in the tumor context may result in an improvement of efficacy of immunotherapeutic approaches.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 207-207
Author(s):  
Steven Scoville ◽  
Bethany Mundy-Bosse ◽  
Michael Zhang ◽  
Li Chen ◽  
Ryan Sanderson ◽  
...  

Abstract Natural killer (NK) cells are innate effector cells that can spontaneously recognize and kill cancer cells. While important in inducing long-term disease free survival (DFS) in the setting of killer immunoglobulin-like receptor (KIR) mismatch for acute myeloid leukemia (AML), harnessing NK cells to kill autologous or self AML blasts to extend DFS has had no success. In this study, we uncover one potential mechanism by which AML blasts can evade NK cell cytotoxicity. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that has now been shown to be expressed in immature human NK cells. Furthermore, activation of AHR in these immature cells suppresses human NK cell maturation and function. We and others have shown that human AML blasts secrete ligands that can activate AHR, leading us to hypothesize that AML may evade autologous NK cell cytotoxicity in part by inhibiting NK cell maturation. Expression of microRNA (miR)-29b has previously been shown to suppress the expression of transcription factors Tbx21 (TBET) and Eomesodermin (EOMES), both of which are critical for terminal NK cell differentiation and function. Here we show that AHR is able to directly regulate the expression of miR-29b and thus may serve as the link between AML and immune evasion of NK cells. We first identified putative AHR binding sites within the proximal promoter of miR-29b, suggesting that AHR may directly regulate miR-29b expression. To test this, we transfected the AHR responsive HepG2 human cell line with a miR-29b promoter driven luciferase reporter and measured luciferase activity after treatment with the known AHR agonist, FICZ, compared to vehicle control. We discovered that cells treated with 6-formylindolol[3,2-b]carbazole (FICZ) had increased luciferase activity compared to cells treated with vehicle control (P<0.05). This effect was subsequently shown to be directly mediated by AHR, as mutation of the putative AHR binding site as well as siRNA targeting of AHR mRNA both significantly diminished the induced luciferase activity (P<0.01). We then established the importance of miR-29b in human NK cell development by transducing immature NK cells, characterized as Lin(-)CD117(+)CD94(-), with a miR-29b knockdown virus and testing for the ability of these cells to become mature [i.e., Lin(-)CD117(-)CD94(+)] NK cells, after two weeks in IL-15 and FICZ. Indeed, in early experiments, knockdown of miR-29b resulted in increased percentages of mature NK cells compared to cells transduced with control virus (16.8% compared to 3.6%, respectively), despite being cultured with an AHR agonist. Finally, utilizing a translational in vivo murine AML model developed by our laboratory that recapitulates human AML, we have found that AML blasts harvested from these leukemic mice release an AHR agonist (P < 0.01), similar to previous reports that have described AHR ligands being produced by human AML blasts. In addition,NK cells isolated from these mice have increased levels of miR-29b when leukemic, compared to NK cells from wild type control littermates, consistent with our hypothesis that AHR regulates miR-29b expression. Thus, we propose that AHR, when activated by AML-derived ligands, upregulates miR-29b in NK cells to ultimately suppress the primary regulators of NK cell maturation and function, resulting in immune evasion (See Figure). Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.


Author(s):  
Khadijeh Dizaji Asl ◽  
Ali Rafat ◽  
Ali Akbar Movassaghpour ◽  
Hojjatollah Nozad Charoudeh ◽  
Hamid Tayefi Nasrabadi

Purpose: Acute myeloid leukemia (AML) is known to be an invasive and highly lethal hematological malignancy in adults and children. Resistance to the present treatments, including radiotherapy and chemotherapy with their side effects and telomere length shortening are the main cause of the mortality in AML patients. Telomeres sequence which are located at the end of eukaryotic chromosome play pivotal role in genomic stability. Recent studies have shown that apoptosis process is blocked in AML patient by the excessive telomerase activity in cancerous blasts. Therefore, the find of effective ways to prevent disease progression has been considered by the researchers. Natural killer (NK) cells as granular effector cells play a critical role in elimination of abnormal and tumor cells. Given that the cytotoxic function of NK cells is disrupted in the AML patients, we investigated the effect of telomerase inhibitors on NK cell differentiation. Methods: To evaluate telomerase inhibition on NK cell differentiation, the expression of CD105, CD56, CD57, and KIRs was evaluated in CD34+ derived NK cells after incubation of them with BIBR1532. Results: The results showed that the expression of CD105, CD56, CD57, and KIRs receptors reduces after telomerase inhibition. According to these findings, BIBR1532 affected the final differentiation of NK cells. Conclusion: The results revealed that telomerase inhibitor drugs suppress cancer cell progression in a NK cells-independent process.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 17-17 ◽  
Author(s):  
Ryan P Sullivan ◽  
Jeffrey W Leong ◽  
Stephanie E Schneider ◽  
Rizwan Romee ◽  
Veronika Sexl ◽  
...  

Abstract Introduction Natural Killer (NK) cells are lymphocytes that are important for early host defense against infectious pathogens and malignant transformation. NK cells differentiate from the CLP in the bone marrow, where they are identified by markers such as CD56 and NKp46 in humans, and NK1.1, CD122, and NKp46 in mice. NK cells further mature in the periphery, and this maturation is essential for NK cell function, as both NK cell cytotoxicity and IFN-g production are dependent upon maturation. NK cell maturation is distinguished by surface marker transitions, including CD56bright to CD56dim in humans, and loss of CD27 expression in mice. However, the factors controlling NK cell differentiation and maturation are incompletely understood. We hypothesized that the transcription factor Myb had a role in this process, due to its high expression in immature NK cells and subsequent loss upon maturation. miRNAs are a family of small RNA molecules that control a wide variety of cellular processes via binding to target sites in the 3'UTR of messenger RNAs and downregulate protein production. The miR-15/16 family is very highly expressed in NK cells, and directly targets the 3'UTR of Myb. We hypothesized that a miR-15a/16-1KO mouse would have NK cell-intrinsic alterations in Myb levels, and would serve as a model of Myb upregulation. Here, we use lentiviral overexpression in primary human and mouse NK cells, as well as an in vitro human NK cell differentiation system, to demonstrate that Myb has critical roles in the NK cell differentiation and maturation processes. Furthermore, we generate a novel mouse model of miR-15/16 deficiency, and show that miR-15/16 is critically important for the regulation of Myb levels, and disruption of miR-15/16 prevents appropriate NK cell maturation. Results and Conclusions In order to investigate the role of Myb in NK cells, we transduced human NK cells, and cultured them in vitro. After 5 days of culture, GFP+ NK cells overexpressing Myb remained CD56bright (84±3 v. 6±2%, p<0.01), whereas NK cells expressing GFP only had differentiated to CD56dim (16±2 v. 94±3%, p<0.001). Mouse CD27+ NK cells were transduced with the same viruses, and adoptively transferred and allowed to mature for 7 days in their new hosts. 0% of NK cells overexpressing Myb matured to CD27-, while 11% of GFP only matured, and 22% of NK cells with knockdown of Myb matured to CD27-. Thus, cells overexpressing Myb have a block in maturation, and Myb downregulation is essential for complete NK cell maturation. To further investigate the role of Myb, we lentivirally transduced and cultured CD34+ progenitors in NK cell differentiation conditions. We found that cells overexpressing Myb had an increased percentage of immature CD56bright NK cells, which arose with more rapid kinetics (91±8 v. 28±16%, p<0.001 at day 14) [Fig. 1]. However, at later time points, cells overexpressing Myb failed to differentiate from CD56bright to the more mature CD56dim NK cells (8±6 v. 64±11%, p<0.01 at day 21). In contrast, CD34 cells transduced with an shRNA directed against Myb, differentiated to CD56dim NK cells more rapidly than control cells (90±7 v. 65±11, p<0.05 at day 21). Therefore, Myb drives initial NK cell differentiation, but prevents final maturation of NK cells. We found that Myb is a direct target of miR-15/16, as overexpression of miR-15/16 reduces the signal of luciferase fused to the 3'UTR of Myb by 50% (p<0.001), while a sponge directed against miR-15/16 increases signal by 40% (p<0.001). Therefore, we generated a novel mouse model of NK cell-specific miR-15a/16-1 knockout driven by NKp46 (Ncr1), and confirmed that Myb expression was increased in miR-15a/16-1KO NK cells (9-fold in CD27+ NK cells, p<0.05). No early differentiation phenotype was observed, because Cre is expressed later, after NK cell lineage determination. In contrast, these mice lacked mature NK cells (31±4 v 62±6 %CD27- of splenic NK, p<0.01, Fig. 2). Additionally, miR-15a/16-1 overexpression in human CD34+ cells recapitulates the phenotype of Myb knockdown, establishing a direct link between miR-15/16 and Myb [Fig. 1]. Therefore, miR-15/16 controls Myb expression in a cell-intrinsic manner, and thereby directs NK cell differentiation and maturation. Disclosures: No relevant conflicts of interest to declare.


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