Interaction of natural killer cells with MHC class II: reversal of HLA-DR1-mediated protection of K562 transfectant from natural killer cell-mediated cytolysis by brefeldin-A

Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation

Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.

Development of combinatorial antibody therapies for diffuse large B cell lymphoma

Diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma, is typically treated with chemotherapy combined with the immunotherapy rituximab, an antibody targeting the B cell receptor, CD20. Despite the success of this treatment regimen, approximately a third of DLBCL patients experience either relapse or have refractory disease that is resistant to rituximab, indicating the need for alternative therapeutic strategies. Here, we identified that CD74 and IL4R are expressed on the cell surface of both CD20 positive and CD20 negative B cell populations. Moreover, genes encoding CD74 and IL4R are expressed in lymphoma biopsies isolated from all stages of disease. We engineered bispecific antibodies targeting CD74 or IL4R in combination with rituximab anti-CD20 (anti-CD74/anti-CD20 and anti-IL4R/anti-CD20). Bispecific antibody function was evaluated by measuring direct induction of apoptosis, antibody-dependent cellular phagocytosis (ADCP), and antibody-dependent cellular cytotoxicity in both rituximab-sensitive and rituximab-resistant DLBCL cell lines. Both anti-CD74/anti-CD20 and anti-IL4R/anti-CD20 were able to mediate ADCC and ADCP, but CD74-targeting therapeutic antibodies could also mediate direct cytotoxicity. Overall, this study strongly indicates that development of bispecific antibodies that target multiple B cell receptors expressed by lymphoma could provide improved defense against relapse and rituximab resistance.

Brefeldin A Induces Apoptosis, Inhibits BCR-ABL Activation, and Triggers BCR-ABL Degradation in Chronic Myeloid Leukemia K562 Cells

BACKGROUND

Chronic myeloid leukemia (CML) is a myeloproliferative disease caused by BCR-ABL oncoprotein. Tyrosine kinase inhibitors have been developed to inhibit the activity of BCR-ABL; however, drug resistance and side effect occur in clinic application. Therefore, it is urgent to find novel drugs for CML treatment. Under the guidance of cytotoxic activity, crude extracts of 55 fungal strains from the medicinal mangrove Acanthus ilicifolius were evaluated, and one potent cytotoxic natural compound, brefeldin A (BFA), was discovered from Penicillium sp. (HS-N-29).

OBJECTIVE

This study was aimed to determine the cytotoxic activity of BFA and the effect on the activation and expression of BCR-ABL in K562 cells.

METHOD

We evaluated cytotoxic activity by MTT assay and soft agar clone assay and apoptosis and cell cycle distribution by Muse cell analyzer. The protein level of BCR-ABL and signaling molecules were detected by western blotting, and the mRNA level of BCR-ABL was determined by RT-PCR.

RESULTS

BFA inhibited cell proliferation, induced G2/M cell cycle arrest, and stimulated cell apoptosis in K562 cells. Importantly, for the first time, we revealed that BFA inhibited the activation of BCR-ABL and consequently inhibited the activation of its downstream signaling molecules in K562 cells. Moreover, we found that BFA degraded BCR-ABL without affecting its transcription in K562 cells, and BFA-induced BCR-ABL degradation was related to caspase activation while not to autophagy or ubiquitinated proteasome degradation pathway.

CONCLUSION

Our present results indicate that BFA acts as a dual functional inhibitor and degrader of BCR-ABL, and BFA is a potential compound for chemotherapeutics to overcome CML.

The SIRPα-CD47 immune checkpoint in NK cells

Here we report on the existence and functionality of the immune checkpoint signal regulatory protein α (SIRPα) in NK cells and describe how it can be modulated for cell therapy. NK cell SIRPα is up-regulated upon IL-2 stimulation, interacts with target cell CD47 in a threshold-dependent manner, and counters other stimulatory signals, including IL-2, CD16, or NKG2D. Elevated expression of CD47 protected K562 tumor cells and mouse and human MHC class I-deficient target cells against SIRPα+ primary NK cells, but not against SIRPα- NKL or NK92 cells. SIRPα deficiency or antibody blockade increased the killing capacity of NK cells. Overexpression of rhesus monkey CD47 in human MHC-deficient cells prevented cytotoxicity by rhesus NK cells in a xenogeneic setting. The SIRPα-CD47 axis was found to be highly species specific. Together, the results demonstrate that disruption of the SIRPα-CD47 immune checkpoint may augment NK cell antitumor responses and that elevated expression of CD47 may prevent NK cell-mediated killing of allogeneic and xenogeneic tissues.

Roles for the FCRL6 Immunoreceptor in Tumor Immunology

Members of the Fc receptor-like (FCRL1-6) gene family encode transmembrane glycoproteins that are preferentially expressed by B cells and generally repress responses via cytoplasmic tyrosine-based regulation. Given their distribution and function, there is a growing appreciation for their roles in lymphoproliferative disorders and as immunotherapeutic targets. In contrast to FCRL1-5, FCRL6 is distinctly expressed outside the B lineage by cytotoxic T and NK lymphocytes. Its restricted expression by these orchestrators of cell-mediated immunity, along with its inhibitory properties and extracellular interactions with MHCII/HLA-DR, represent a newly appreciated axis with relevance in tolerance and cancer defense. The significance of FCRL6 in this arena has been recently demonstrated by its upregulation in HLA-DR⁺ tumor samples from melanoma, breast, and lung cancer patients who relapsed following PD-1 blockade. These findings imply a potential mechanistic role for FCRL6 in adaptive evasion to immune checkpoint therapy. Here we review these new developments in the FCRL field and identify new evidence for the prognostic significance of FCRL6 in malignancies that collectively indicate its potential as a biomarker and therapeutic target.

Regulation of NK-Cell Function by HLA Class II

Natural Killer (NK) cells were initially described as part of the innate immune system and characterized by their ability to lyse malignant and virus-infected cells. The cytolytic function of NK cells is tightly controlled by activating and inhibitory receptors expressed on the cell surface. Ligands that interact with a variety of NK-cell receptors include the human leukocyte antigen (HLA) molecules, and the regulation of NK-cell function by HLA class I molecules is well-established. Earlier studies also suggested a role of HLA class II molecules in regulating NK cell activity; yet, interactions between HLA class II molecules and NK cell receptors have not been well-characterized. We recently identified a subset of HLA-DP molecules that can serve as ligands for the natural cytotoxicity receptor NKp44 and activate NK cells. This novel receptor-ligand interaction provides a potential mechanism to explain the strong associations of HLA-DP molecules with HBV infection outcomes, graft-vs.-host disease and inflammatory bowel disease. Furthermore, it adds a new mechanism for NK-cell crosstalk with immune cells expressing HLA class II molecules. In this perspective article, we discuss the potential implications of NK cell receptor interactions with HLA class II molecules for the regulation of immune responses.

A subset of HLA-DP molecules serve as ligands for the natural cytotoxicity receptor NKp44

Natural killer (NK) cells can recognize virus-infected and stressed cells¹ using activating and inhibitory receptors, many of which interact with HLA class I. Although early studies also suggested a functional impact of HLA class II on NK cell activity^2,3, the NK cell receptors that specifically recognize HLA class II molecules have never been identified. We investigated whether two major families of NK cell receptors, killer-cell immunoglobulin-like receptors (KIRs) and natural cytotoxicity receptors (NCRs), contained receptors that bound to HLA class II, and identified a direct interaction between the NK cell receptor NKp44 and a subset of HLA-DP molecules, including HLA-DP401, one of the most frequent class II allotypes in white populations⁴. Using NKp44ζ⁺ reporter cells and primary human NKp44⁺ NK cells, we demonstrated that interactions between NKp44 and HLA-DP401 trigger functional NK cell responses. This interaction between a subset of HLA-DP molecules and NKp44 implicates HLA class II as a component of the innate immune response, much like HLA class I. It also provides a potential mechanism for the described associations between HLA-DP subtypes and several disease outcomes, including hepatitis B virus infection^5-7, graft-versus-host disease⁸ and inflammatory bowel disease^9,10.

Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement

Immunotherapies targeting the PD-1 pathway produce durable responses in many cancers, but the tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II expression on tumor cells can predict response to anti-PD-1 therapy. We therefore sought to determine how MHC-II expression by tumor cells promotes PD-1 dependency. Using transcriptional profiling of anti-PD-1-treated patients, we identified unique patterns of immune activation in MHC-II+ tumors. In patients and preclinical models, MHC-II+ tumors recruited CD4+ T cells and developed dependency on PD-1 as well as Lag-3 (an MHC-II inhibitory receptor), which was upregulated in MHC-II+ tumors at acquired resistance to anti-PD-1. Finally, we identify enhanced expression of FCRL6, another MHC-II receptor expressed on NK and T cells, in the microenvironment of MHC-II+ tumors. We ascribe this to what we believe to be a novel inhibitory function of FCRL6 engagement, identifying it as an immunotherapy target. These data suggest a MHC-II-mediated context-dependent mechanism of adaptive resistance to PD-1-targeting immunotherapy.

Tumor-specific MHC-II expression drives a unique pattern of resistance to immunotherapy via LAG-3/FCRL6 engagement

Immunotherapies targeting the PD-1 pathway produce durable responses in many cancers, but the tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II expression on tumor cells can predict response to anti-PD-1 therapy. We therefore sought to determine how MHC-II expression by tumor cells promotes PD-1 dependency. Using transcriptional profiling of anti-PD-1-treated patients, we identified unique patterns of immune activation in MHC-II+ tumors. In patients and preclinical models, MHC-II+ tumors recruited CD4+ T cells and developed dependency on PD-1 as well as Lag-3 (an MHC-II inhibitory receptor), which was upregulated in MHC-II+ tumors at acquired resistance to anti-PD-1. Finally, we identify enhanced expression of FCRL6, another MHC-II receptor expressed on NK and T cells, in the microenvironment of MHC-II+ tumors. We ascribe this to what we believe to be a novel inhibitory function of FCRL6 engagement, identifying it as an immunotherapy target. These data suggest a MHC-II-mediated context-dependent mechanism of adaptive resistance to PD-1-targeting immunotherapy.

Extracellular vesicles as emerging targets in cancer: Recent development from bench to bedside

Extracellular vesicles (EVs) have emerged as important players of cancer initiation and progression through cell-cell communication. They have been recognized as critical mediators of extracellular communications, which promote transformation, growth invasion, and drug-resistance of cancer cells. Interestingly, the secretion and uptake of EVs are regulated in a more controlled manner than previously anticipated. EVs are classified into three groups, (i) exosomes, (ii) microvesicles (MVs), and (iii) apoptotic bodies (ABs), based on their sizes and origins, and novel technologies to isolate and distinguish these EVs are evolving. The biologically functional molecules harbored in these EVs, including nucleic acids, lipids, and proteins, have been shown to induce key signaling pathways in both tumor and tumor microenvironment (TME) cells for exacerbating tumor development. While tumor cell-derived EVs are capable of reprogramming stromal cells to generate a proper tumor cell niche, stromal-derived EVs profoundly affect the growth, resistance, and stem cell properties of tumor cells. This review summarizes and discusses these reciprocal communications through EVs in different types of cancers. Further understanding of the pathophysiological roles of different EVs in tumor progression is expected to lead to the discovery of novel biomarkers in liquid biopsy and development of tumor specific therapeutics. This review will also discuss the translational aspects of EVs and therapeutic opportunities of utilizing EVs in different cancer types.

The human ortholog of granulocyte macrophage colony-stimulating factor and interleukin-2 fusion protein induces potent ex vivo natural killer cell activation and maturation

Natural killer (NK) cells are appealing cellular pharmaceuticals for cancer therapy because of their innate ability to recognize and kill tumor cells. Therefore, the development of methods that can enhance the potency in their anticancer effect would be desirable. We have previously shown that a murine granulocyte macrophage colony-stimulating factor (GM-CSF)/interleukin 2 (IL-2) fusion protein displays novel antitumor properties in vivo compared with both cytokines in combination due to recruitment of NK cells. In the present work, we have found that human ortholog of the GM-CSF/IL-2 fusion protein (a.k.a. hGIFT2) induces robust NK cell activation ex vivo with significant secretion of RANTES and a 37-fold increase in IFNgamma production when compared with either IL-2 or GM-CSF single cytokine treatment or their combination. Moreover, hGIFT2 upregulates the expression of NK cell activating receptors NKp44, NKp46, and DNAM-1 (CD226), as well as CD69, CD107a, and IL-2Rbeta expression. In addition, hGIFT2 promotes NK cell maturation, based on the downregulation of CD117 expression and upregulation of CD11b. This phenotype correlates with significantly greater cytotoxicity against tumor cells. At the molecular level, hGIFT2 leads to a potent activation of Janus-activated kinases (JAK) downstream of both IL-2 and GM-CSF receptors (JAK1 and JAK2, respectively) and consequently leads to a hyperphosphorylation of signal transducers and activators of transcription (STAT)1, STAT3, and STAT5. In conclusion, hGIFT2 fusokine possesses unique biochemical properties distinct from IL-2 and GM-CSF, constitutes a novel and potent tool for ex vivo NK cell activation and maturation, and may be of use for cancer cell immunotherapy.

Donor lymphocyte infusions for acute myeloid leukaemia

The success of donor lymphocyte infusion (DLI) in treating chronic myeloid leukaemia that had recurred after allogeneic haematopoietic stem cell transplantation provided direct evidence for the existence of an immunologically mediated graft-vs-leukaemia effect and led to the development of non-myeloablative transplantation. For patients with acute myeloid leukaemia (AML), DLI has been less effective, both as a result of its rapid growth kinetics and its decreased susceptibility to alloimmune-mediated effects. This chapter reviews the historical experience with DLI for AML, both as treatment for and prophylaxis of relapse. New approaches aimed at improving the efficacy of DLI are discussed, including administration of chemotherapy prior to DLI, use of immunomodulatory cytokines to bolster the cytotoxic effector response, priming of donor lymphocytes to recipient tumour antigens ex vivo, and infusions of alloreactive natural killer cells.

Acute laryngotracheitis in the rat induced by Sendai virus: the influx of six different types of immunocompetent cells into the laryngeal mucosa differs strongly between the subglottic and the glottic compartment

OBJECTIVES

Acute laryngotracheitis is a disease in which mainly the subglottic area is infected, whereas adjacent parts of the larynx, especially the narrow glottic fold, remain unaffected. The reason for the difference between these two directly adjacent regions is unknown. Therefore, in the present study the influx of dendritic cells, neutrophils, T and B lymphocytes, natural killer cells, and macrophages into the mucosa of different laryngeal compartments was investigated after Sendai virus infection in the rat. The aims were to study both the influx of immunocompetent cells and the adhesion of the pathogen and to correlate them to the different reactions of the laryngeal areas during pseudocroup.

METHODS

Acute laryngotracheitis was induced by intranasal application of Sendai virus in brown Norway rats. This virus is exclusively pneumotropic in rodents and belongs to the parainfluenza virus type 1, the main pathogen of acute laryngotracheitis in children. The numbers of dendritic cells, neutrophils, T and B lymphocytes, natural killer cells, and macrophages were determined in the supraglottic, glottic, subglottic, and tracheal mucosa on days 2, 5, 7, and 14 after virus application. Furthermore, the nucleoprotein of the virus and major histocompatibility complex (MHC) Class II expression were detected immunohistologically on the laryngeal epithelium.

RESULTS

All cell subsets entered the laryngeal mucosa during inflammation. The highest influx was detected among dendritic cells subglottically. This was accompanied by a strong virus adhesion and MHC Class II expression on the subglottic epithelium. In contrast, only a few immunocompetent cells entered the adjacent glottic mucosa, and on the glottic epithelium staining for virus nucleoprotein and MHC Class II expression was weak.

CONCLUSIONS

The inflammatory response of the laryngeal mucosa shows great regional differences in this animal model during experimental viral infection. The response was characterized by a strong subglottic and a weak glottic reaction. A possible reason for this difference might be region-specific viral adhesion on the epithelium of the laryngeal areas, as well as differences in MHC Class II expression. Thus, these data agree with the clinical observation during acute laryngotracheitis and may explain why the subglottic part of the larynx is affected preferentially during pseudocroup. The molecular mechanisms mediating the different reactions await clarification.

LAG-3 does not define a specific mode of natural killing in human

LAG-3 is a gene localized on the band p13 of human chromosome 12, close to the NK gene complex (NKC), expressed on activated NK cells and encoding a receptor for MHC class II molecules. Recently, LAG-3 has been proposed to define a specific mode of natural killing in mice. The putative role of LAG-3 on human natural killer cytotoxicity has been examined with specific monoclonal antibodies and a recombinant soluble form of LAG-3. Neither the antibodies, which are able to block the interaction with the ligand, nor the recombinant product, which has retained its binding capacity for MHC class II, had an effect on the natural killing of various target cells. Furthermore, in redirected killing assays, none of these antibodies were able to modulate either positively or negatively the cytotoxicity. Taken together, these data show that LAG-3 has no transducing activity involved in NK cytotoxicity, ruling out the existence of a specific mode of natural killing defined by this molecule in humans.

Regulation of a Graft-Versus-Leukemia Effect by Major Histocompatibility Complex Class II Molecules on Leukemia Cells: HLA-DR1 Expression Renders K562 Cell Tumors Resistant to Adoptively Transferred Lymphocytes in Severe Combined Immunodeficiency Mice/Nonobese Diabetic Mice

To understand the role of key molecules in determining the strength and nature of allogeneic T-cell response to leukemia, we transfected HLA-DR1 into the major histocompatibility complex (MHC)-deficient, natural killer (NK)-cell sensitive K562 leukemia cell line. Untransfected K562 cells stimulated NK proliferation in vitro and formed subcutaneous tumors in severe combined immunodeficiency/non-obese diabetic (SCID/NOD) mice. Tumor growth was inhibited by adoptive intravenous transfer of fresh unprimed peripheral blood mononuclear cells (PBMC). In contrast, HLA-DR1 transfected cells stimulated CD4+ T cells, but not NK-cell proliferation in vitro and formed tumors resistant to fresh PBMC in SCID/NOD mice. Tumors not expressing MHC were infiltrated with CD16+CD56+ lymphocytes whereas nonregressing HLA-DR1 expressing tumors showed only a scanty infiltration with both T-cell and NK-cell subsets. The results indicate that MHC class II expression by leukemia cells can determine the effector cell type that it engages. In vivo MHC class II expression rendered K562 cell tumors resistant to NK-cell mediated antitumor reactivity.

Regulation of a Graft-Versus-Leukemia Effect by Major Histocompatibility Complex Class II Molecules on Leukemia Cells: HLA-DR1 Expression Renders K562 Cell Tumors Resistant to Adoptively Transferred Lymphocytes in Severe Combined Immunodeficiency Mice/Nonobese Diabetic Mice

To understand the role of key molecules in determining the strength and nature of allogeneic T-cell response to leukemia, we transfected HLA-DR1 into the major histocompatibility complex (MHC)-deficient, natural killer (NK)-cell sensitive K562 leukemia cell line. Untransfected K562 cells stimulated NK proliferation in vitro and formed subcutaneous tumors in severe combined immunodeficiency/non-obese diabetic (SCID/NOD) mice. Tumor growth was inhibited by adoptive intravenous transfer of fresh unprimed peripheral blood mononuclear cells (PBMC). In contrast, HLA-DR1 transfected cells stimulated CD4+ T cells, but not NK-cell proliferation in vitro and formed tumors resistant to fresh PBMC in SCID/NOD mice. Tumors not expressing MHC were infiltrated with CD16+CD56+ lymphocytes whereas nonregressing HLA-DR1 expressing tumors showed only a scanty infiltration with both T-cell and NK-cell subsets. The results indicate that MHC class II expression by leukemia cells can determine the effector cell type that it engages. In vivo MHC class II expression rendered K562 cell tumors resistant to NK-cell mediated antitumor reactivity.

Inflammatory infiltration of the upper airway epithelium during Sendai virus infection: involvement of epithelial dendritic cells

We undertook the present study to determine the nature of the cellular inflammatory response within the epithelial lining of the rat trachea during a Sendai virus infection. In particular, we aimed to investigate changes in the resident population of epithelial dendritic cells. Rats were infected with Sendai virus, and tracheal tissue was examined immunohistochemically at various times with a panel of cell-specific monoclonal antibodies. We found that Sendai virus infection was restricted to only the lumenal layer of epithelial cells and that virus nucleoprotein was present from days 2 to 5 postinfection. Starting around day 2 or 3, there was a large cellular influx consisting of macrophages, neutrophils, NK cells, and T cells; this coincided with expression of high levels of ICAM-1 on the basal (uninfected) layers of the epithelium. The T cells were mostly alphabeta T-cell receptor positive; however, a smaller influx of gammadelta T cells also took place. The number of resident dendritic cells increased markedly during infection, with numbers peaking around day 5 and remaining elevated 14 days later. The peak of the inflammatory response occurred on day 5 and declined thereafter, with the exception of dendritic cell and alphabeta T-cell numbers, which remained elevated. Starting around day 3, the tracheal epithelial cells expressed increasing levels of major histocompatibility complex class II antigen. This expression was maximal at day 5 and declined rapidly thereafter. In vitro culture of tracheal segments demonstrated that viral infection was not per se responsible for the upregulation of class II expression and that when cultured in the presence of gamma interferon, class II antigen was induced on epithelial cells.

Mechanisms of the graft-versus-leukemia reaction

It is now clear that the graft-versus-leukemia (GVL) effect which accompanies allogeneic bone marrow transplantation for hematological malignancies is a powerful therapeutic weapon which, if harnessed, could improve our ability to treat refractory malignant disorders. Advances in the understanding of the alloimmune response now provide a clearer picture of the mechanisms involved in the GVL reaction: the CD4+ T cell plays a central role in the orchestration of leukemia cell killing. The immunogenicity of the leukemia is also a major factor determining the effectiveness of the GVL response. The characterization of antigens restricted to leukemia and hematopoietic tissues should make it eventually possible to produce specific and powerful antileukemic alloresponses in donor lymphocytes by adoptive immunotherapy or by vaccines.

Killer cell inhibitory receptor interactions with HLA class I molecules: implications for alloreactivity and transplantation

Human killer cell inhibitory receptors (KIR) are novel members of the immunoglobulin superfamily of cell surface glycoproteins, which are expressed by lymphocytes with natural killers (NK) and cytotoxic T-cell (CTL) phenotypes. These receptors have specificity for relatively conserved epitopes of HLA-A, -B, and -C class I antigens. Recent studies have identified KIR as being involved in the transmission of negative, inhibitory signaling events to the cytotoxic cell which prevent or diminish target cell lysis. KIR are thus likely to play an important role in the responses of alloreactive NK cells and CTL to allogeneic HLA antigens. In this article, we review the known structural and functional characteristics of KIR, suggest a possible mechanism for the transmission of intracellular negative signaling by these receptors, and discuss the relevance of KIR function and HLA specificity to the clinical transplantation of allogeneic tissues.