A Transcriptional Signature of IL-2 Expanded Natural Killer Cells Predicts More Favorable Prognosis in Bladder Cancer

Activation of natural killer (NK) cell function is regulated by cytokines, such as IL-2, and secreted factors upregulated in the tumor microenvironment, such as platelet-derived growth factor D (PDGF-DD). In order to elucidate a clinical role for these important regulators of NK cell function in antitumor immunity, we generated transcriptional signatures representing resting, IL-2-expanded, and PDGF-DD-activated, NK cell phenotypes and established their abundance in The Cancer Genome Atlas bladder cancer (BLCA) dataset using CIBERSORT. The IL-2-expanded NK cell phenotype was the most abundant in low and high grades of BLCA tumors and was associated with improved prognosis. In contrast, PDGFD expression was associated with numerous cancer hallmark pathways in BLCA tumors compared with normal bladder tissue, and a high tumor abundance of PDGFD transcripts and the PDGF-DD-activated NK cell phenotype were associated with a poor BLCA prognosis. Finally, high tumor expression of transcripts encoding the activating NK cell receptors, KLRK1 and the CD160–TNFRSF14 receptor–ligand pair, was strongly correlated with the IL-2-expanded NK cell phenotype and improved BLCA prognosis. The transcriptional parameters we describe may be optimized to improve BLCA patient prognosis and risk stratification in the clinic and potentially provide gene targets of therapeutic significance for enhancing NK cell antitumor immunity in BLCA.

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Identification of Potential Diagnostic Genes for Bladder Cancer by Bioinformatic Analysis

10.21203/rs.3.rs-978784/v1 ◽

2021 ◽

Author(s):

Yongxing Peng ◽

Minqin Mao ◽

Zhonglai Li ◽

Qipeng Xia ◽

Honghua Tong

Keyword(s):

Gene Expression ◽

Bladder Cancer ◽

Area Under The Curve ◽

Bioinformatic Analysis ◽

The Cancer Genome Atlas ◽

High Rate ◽

Diagnostic Efficiency ◽

Bladder Tissue ◽

Diagnostic Efficacy ◽

Normal Bladder

Abstract Background: Cytology and transurethral cystoscopy constitute the gold standard for the diagnosis of bladder cancer (BC). However, some minor lesions cannot be detected in time with these techniques, resulting in a high rate of missed diagnosis. Finding biomarkers that are economical, convenient, sensitive, and specific has become an urgent priority.Methods: Gene expression profile data from BC and normal bladder tissue were downloaded from the Gene Expression Omnibus (GEO) database and used as a training set to screen for differentially expressed genes (DEGs). The bladder gene expression and related clinical data derived from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used as a validation set. The effectiveness of the DEGs as diagnostic criteria was verified in terms of gene expression, gene mutation and diagnostic efficiency.Results: Two upregulated and eight downregulated hub genes were identified by screening. In terms of gene expression, the expression levels of these genes were significantly different between bladder cancer tissues and normal tissues. In terms of clinical diagnostic efficacy, TOP2A had the highest single diagnostic value, while the combinations of TOP2A/CNN1, TOP2A/ISG15/CNN1 and TOP2AISG15/ACTG2 had the largest area under the curve (AUC) among two- or three-indicator combinations.Conclusion: TOP2A, either alone or as part of a combination, has notable diagnostic advantages. However, this still needs to be confirmed in a larger sample with further biological experiments.

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NK cell function is impaired during long-duration spaceflight

Journal of Applied Physiology ◽

10.1152/japplphysiol.00761.2018 ◽

2019 ◽

Vol 126 (4) ◽

pp. 842-853 ◽

Cited By ~ 10

Author(s):

Austin B. Bigley ◽

Nadia H. Agha ◽

Forrest L. Baker ◽

Guillaume Spielmann ◽

Hawley E. Kunz ◽

...

Keyword(s):

Immune System ◽

Nk Cells ◽

Natural Killer ◽

Cell Function ◽

Nk Cell ◽

Crew Member ◽

Cell Phenotype ◽

Cell Mediated Immunity ◽

Space Travel ◽

Long Duration

Maintaining astronaut health during space travel is paramount for further human exploration of the solar system beyond Earth’s orbit. Of concern are potential dysregulations in immunity, which could increase the likelihood of cancer and latent viral reactivation. Natural killer (NK) cells are critical effectors of the innate immune system, and their function and phenotype are important to immunosurveillance of nascent tumors and latent viral infections. We compared changes in NK cell phenotype and function in eight crew members who completed an ~6-mo mission to the International Space Station (ISS) with healthy controls who remained on Earth. Assessments were made before (180 and 60 days before launch), during [flight day + 90 days (FD+90) and 1 day before return (R−1)], and after the mission (at R+0, R+18, R+33, and R+66). These samples, plus an additional in-flight sample (FD+180), were collected from a crew member who spent 340 days (~1 yr) on the ISS. NK cell cytotoxic activity (NKCA) against K562 leukemia targets in vitro was reduced by ~50% at FD+90 in ISS crew but not controls. This decrease was more pronounced in “rookie” compared with “veteran” crew members. The ~1-yr mission crew member did not show declines in NKCA against K562 until late in the mission (R−1 and R+0). NK cell numbers, expression of activating and inhibitory receptors, target cell binding, and expression and degranulation of perforin and granzyme B were unaltered with spaceflight. Similarly, when we exposed an immortalized NK cell line (NK-92) to sera collected at different mission time points (before, during, and after flight), there was no effect on NKCA. This is the first study to report impaired NK cell function during long-duration space travel. Countermeasures may be needed to mitigate immune system impairment in exploration class mission crew during long-duration spaceflight missions. NEW & NOTEWORTHY Immune system impairment may inhibit future human space exploration missions to Mars. Natural killer (NK) cells are key components of immunity and vital for tumor surveillance and the prevention of latent virus reactivation. We report that NK cell function is impaired in astronauts during an ~6-mo orbital space mission compared with preflight levels and ground-based controls. Declines in NK cell function were more marked in first-time “rookie” fliers. Countermeasures are needed to preserve NK cell-mediated immunity during spaceflight.

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Charge-Altering Releasable Transporters Enable Specific Phenotypic Manipulation of Resting Primary Natural Killer Cells

10.1101/2020.02.28.970491 ◽

2020 ◽

Cited By ~ 1

Author(s):

Aaron J. Wilk ◽

Nancy L. Benner ◽

Rosemary Vergara ◽

Ole A.W. Haabeth ◽

Ronald Levy ◽

...

Keyword(s):

Nk Cells ◽

Natural Killer ◽

Cell Activation ◽

Cell Function ◽

Nk Cell ◽

Clinical Applications ◽

Cell Manipulation ◽

Cell Phenotype ◽

Phenotypic Manipulation ◽

And Function

ABSTRACTNatural killer (NK) cells are capable of rapid and robust cytotoxicity, making them excellent tools for immunotherapy. However, their recalcitrance to standard transfection techniques has limited both mechanistic studies and clinical applications. Current approaches for NK cell manipulation rely on viral transduction or methods requiring NK cell activation, which can alter NK cell function. Here, we report that non-viral Charge-Altering Releasable Transporters (CARTs) efficiently transfect primary human NK cells with mRNA without relying on NK cell activation. Compared to electroporation, CARTs transfect NK cells two orders of magnitude more efficiently, better preserve cell viability, and cause minimal reconfiguration of NK cell phenotype and function. Finally, we use CARTs to generate highly cytotoxic primary human chimeric antigen receptor NK cells, indicating potential therapeutic utility of this technique. To our knowledge, CARTs represent the first efficacious transfection technique for resting primary NK cells that preserves NK cell phenotype, and can drive new biological discoveries and clinical applications of this understudied lymphocyte subset.

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Immunomodulation of the Natural Killer Cell Phenotype and Response during HCV Infection

Journal of Clinical Medicine ◽

10.3390/jcm9041030 ◽

2020 ◽

Vol 9 (4) ◽

pp. 1030 ◽

Cited By ~ 5

Author(s):

Gaitan Fabrice Njiomegnie ◽

Scott A. Read ◽

Nicole Fewings ◽

Jacob George ◽

Fiona McKay ◽

...

Keyword(s):

Nk Cells ◽

Natural Killer ◽

Chronic Infection ◽

Cell Function ◽

Nk Cell ◽

Acute Infection ◽

Killer Cell ◽

Innate Immune ◽

Hcv Infection ◽

Cell Phenotype

Hepatitis C virus (HCV) infection develops into chronic hepatitis in over two-thirds of acute infections. While current treatments with direct-acting antivirals (DAAs) achieve HCV eradication in >95% of cases, no vaccine is available and re-infection can readily occur. Natural killer (NK) cells represent a key cellular component of the innate immune system, participating in early defence against infectious diseases, viruses, and cancers. When acute infection becomes chronic, however, NK cell function is altered. This has been well studied in the context of HCV, where changes in frequency and distribution of NK cell populations have been reported. While activating receptors are downregulated on NK cells in both acute and chronic infection, NK cell inhibiting receptors are upregulated in chronic HCV infection, leading to altered NK cell responsiveness. Furthermore, chronic activation of NK cells following HCV infection contributes to liver inflammation and disease progression through enhanced cytotoxicity. Consequently, the NK immune response is a double-edged sword that is a significant component of the innate immune antiviral response, but persistent activation can drive tissue damage during chronic infection. This review will summarise the role of NK cells in HCV infection, and the changes that occur during HCV therapy.

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Natural Killer Cell Function Tests by Flowcytometry-Based Cytotoxicity and IFN-γ Production for the Diagnosis of Adult Hemophagocytic Lymphohistiocytosis

International Journal of Molecular Sciences ◽

10.3390/ijms20215413 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5413 ◽

Cited By ~ 4

Author(s):

Lee ◽

Kim ◽

Lee ◽

Park ◽

Choi ◽

...

Keyword(s):

Natural Killer ◽

Hemophagocytic Lymphohistiocytosis ◽

Cell Function ◽

Nk Cell ◽

Cell Phenotype ◽

Cytotoxicity Test ◽

Serum Cytokine ◽

Function Tests ◽

Cytokine Levels ◽

Nk Cytotoxicity

Although natural killer (NK) cell function is a hallmark of hemophagocytic lymphohistiocytosis (HLH), there is no standard method or data on its diagnostic value in adults. Thus, we performed a single-center retrospective study of 119 adult patients with suspected HLH. NK cell function was determined using both flowcytometry-based NK-cytotoxicity test (NK-cytotoxicity) and NK cell activity test for interferon-gamma (NKA-IFNγ). NK cell phenotype and serum cytokine levels were also tested. Fifty (42.0%) HLH patients showed significantly reduced NK cell function compared to 69 non-HLH patients by both NK-cytotoxicity and NKA-IFNγ (p < 0.001 and p = 0.020, respectively). Agreement between NK-cytotoxicity and NKA-IFNγ was 88.0% in HLH patients and 58.0% in non-HLH patients. NK-cytotoxicity and NKA-IFNγ assays predicted HLH with sensitivities of 96.0% and 92.0%, respectively. The combination of NKA-IFNγ and ferritin (>10,000 µg/L) was helpful for ruling out HLH, with a specificity of 94.2%. Decreased NK-cytotoxicity was associated with increased soluble IL-2 receptor levels and decreased CD56dim NK cells. Decreased NKA-IFNγ was associated with decreased serum cytokine levels. We suggest that both NK-cytotoxicity and NKA-IFNγ could be used for diagnosis of HLH. Further studies are needed to validate the diagnostic and prognostic value of NK cell function tests.

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N6-Methylandenosine-Related lncRNAs are Potential Biomarkers for Predicting the Overall Survival Rate of Patients Bladder Cancer

10.21203/rs.3.rs-534193/v1 ◽

2021 ◽

Author(s):

Haihang Zhang ◽

Panpan Xie ◽

Kaijia Shi ◽

Danni Xu ◽

Xingrui Cai ◽

...

Keyword(s):

Bladder Cancer ◽

Prognostic Value ◽

Immune Cell ◽

Cox Regression ◽

Pearson Correlation ◽

Prognostic Significance ◽

The Cancer Genome Atlas ◽

Bladder Tissue ◽

Cox Regression Analysis ◽

Normal Bladder

Abstract Background: The prognostic value of N6-methylandenosine-related long non-coding RNAs (m6A-related lncRNAs) was investigated in 414 bladder cancer (BLCA) and 19 normal bladder tissue samples from The Cancer Genome Atlas (TCGA) datasets. Methods: We implemented Pearson correlation analysis to explore the lncRNAs associated with m6A, and then performed univariate Cox regression analysis to identify nine m6A-associated lncRNAs with prognostic value. The patients with BLCA were divided into two subgroups by consistency clustering. Analysis of the two groups of immune cell infiltration, immune microenvironment and clinical results were significantly different. We identified the prognostic significance of m6A-related lncRNAs by bioinformatic and statistical analysis of data from patients with BLCA.Results: We constructed an m6A-related lncRNA prognostic signature (m6A-LPS, including AL136295.2, AC104564.3, ATP1B3-AS1, EHMT2-AS1 and AC116914.2) to predict the OS of BLCA patients. It is proved that m6A LPS has independent prognostic value.

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Identification and Enrichment of Proteolytic Enzymes of IL-2 Activated Rat Natural Killer (A-NK) Cells: Potential Physiological Roles in NK Cell Function

Tumor Immunology and Cancer Therapy ◽

10.1201/9781003067245-10 ◽

2020 ◽

pp. 83-92

Author(s):

Richard P. Kitson ◽

Ken Wasserman ◽

Ronald H. Goldfarb

Keyword(s):

Nk Cells ◽

Natural Killer ◽

Cell Function ◽

Nk Cell ◽

Proteolytic Enzymes

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217 Cytotoxicity of nicotinamide enhanced natural killer cells GDA201 is based on metabolic modulation as demonstrated by artificial intelligence assisted analysis of NK cell transcriptome and metabolome

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2021-sitc2021.217 ◽

2021 ◽

Vol 9 (Suppl 3) ◽

pp. A230-A230

Author(s):

Dima Yackoubov ◽

Aviad Pato ◽

Julia Rifman ◽

Sherri Cohen ◽

Astar Hailu ◽

...

Keyword(s):

Artificial Intelligence ◽

Machine Learning ◽

Informed Consent ◽

Nk Cells ◽

Natural Killer ◽

Cell Function ◽

Nk Cell ◽

Medical Center ◽

Enzymatic Reactions ◽

Combined Algorithm

BackgroundNicotinamide (NAM), an allosteric inhibitor of NAD-dependent enzymes, has been shown to preserve cell function and prevent differentiation in ex vivo cell culture. GDA-201 is an investigational natural killer (NK) cell immunotherapy derived from allogeneic donors and expanded using IL-15 and NAM. In previous preclinical studies, NAM led to increased homing and cytotoxicity, preserved proliferation, and enhanced tumor reduction of NK cells. In a phase I clinical trial, treatment with GDA-201 showed tolerability and clinical responses in patients with refractory non-Hodgkin lymphoma (NHL) (Bachanova, et. al., Blood 134:777, 2019). While NAM is known to affect cellular metabolism and participate in 510 enzymatic reactions −in 66 as an inhibitor or activator− its mechanism of action and role in GDA-201 cytotoxicity is unknown.MethodsIn order to define the network of intracellular interactions that leads to the GDA-201 phenotype, flow-cytometry, next generation sequencing (NGS), and liquid chromatography–mass spectrometry (LC-MS)-based metabolite quantification were performed on NK cells cultured for 14 days with IL-15 and human serum in the presence or absence of NAM (7 mM). Artificial Intelligence (AI) machine learning analysis was applied by Pomicell in order to analyze the data using the Pomicell databases supporting data extracted from multiple origins including scientific articles organized using natural language processing tools. AI training was done using a combined algorithm designed to blindly explain and predict the transcriptomic and metabolomic (omics) profile.ResultsOmics analyses defined 1,204 differentially expressed genes, and 100 significantly modified metabolites in the presence of NAM. An in silico model was created that successfully predicted the experimental data in 83% of the cases. Upregulation of TIM-3 expression in GDA-201 was predicted to be mediated by inhibition of IL-10 and SIRT3, via CREB1/HLA-G signaling and adrenoceptor beta 2 (ADRB2) upregulation. Adenosine metabolite reduction supports this and suggests dopaminergic activation of NK cytotoxicity. Upregulation of CD62L in the presence of NAM was predicted to be mediated by transcription factor Dp-1 (TFDP1) via dihydrofolate reductase (DHFR) activation and intracellular folic acid reduction. Interferon-gamma and CASP3 modulation (via JUN and MCL1, respectively), via PPARa inhibition, support that finding.ConclusionsIn conclusion, AI machine learning of transcriptome and metabolome data revealed multiple pleiotropic metabolic pathways modulated by NAM. These data serve to further elucidate the mechanism by which NAM enhances cell function, leading to the observed cytotoxicity and potency of GDA-201.Ethics ApprovalWe hereby declare that the collection of the Apheresis units in the three participating institutes (sites) has been done under an approved clinical study that meets the following requirements:1. Ethics approval has been obtained from the local EC at each of the sites, prior to any study related activities.2. The working procedures of the EC at the sites for conduct of clinical studies are in due compliance with local regulations (Israeli Ministry of Health) and provisions of Harmonized International Guidelines for Good Clinical Practice, namely: ICH-GCP.3. Sites follow EC conditions & requirements in terms of submissions, notifications, and approval renewals. 4. Participants gave Informed Consent (approved by the EC) before taking part in the study.5. Informed Consent has been approved by the ECs. The Israeli template of Informed Consent is in used and it includes study specific information (e.g. study goal, design, method, duration, risks, etc.). Name of the Institute Name of the EC/IRB EC Study No.Hadassah Medical Center Helsinki Committee 0483-16-HMORambam Health Care Campus Helsinki Committee 0641-18-RMBIchilov Sourasky Medical Center Tel-Aviv Helsinki Committee 0025-17-TLV

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Natural Killer Cells in the Malignant Niche of Multiple Myeloma

Frontiers in Immunology ◽

10.3389/fimmu.2021.816499 ◽

2022 ◽

Vol 12 ◽

Author(s):

Ondrej Venglar ◽

Julio Rodriguez Bago ◽

Benjamin Motais ◽

Roman Hajek ◽

Tomas Jelinek

Keyword(s):

Multiple Myeloma ◽

Nk Cells ◽

Natural Killer ◽

Defense Mechanisms ◽

Hematological Malignancies ◽

Cell Function ◽

Nk Cell ◽

Current Knowledge ◽

Suppressor Activity ◽

Infected Cells

Natural killer (NK) cells represent a subset of CD3- CD7+ CD56+/dim lymphocytes with cytotoxic and suppressor activity against virus-infected cells and cancer cells. The overall potential of NK cells has brought them to the spotlight of targeted immunotherapy in solid and hematological malignancies, including multiple myeloma (MM). Nonetheless, NK cells are subjected to a variety of cancer defense mechanisms, leading to impaired maturation, chemotaxis, target recognition, and killing. This review aims to summarize the available and most current knowledge about cancer-related impairment of NK cell function occurring in MM.

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