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Xiao W, Yu K, Deng X, Zeng Y. Natural killer cell-associated prognosis model characterizes immune landscape and treatment efficacy of diffuse large B cell lymphoma. Cytokine 2024; 182:156726. [PMID: 39111113 DOI: 10.1016/j.cyto.2024.156726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/25/2024]
Abstract
PURPOSE NK cells are essential for the detection, identification and prediction of cancer. However, so far, there is no prognostic risk model based on NK cell-related genes to predict the prognosis and treatment outcome of DLBCL patients. This study aimed to explore a risk assessment model that could accurately predict the prognosis and treatment efficacy of DLBCL. METHODS Bioinformatics analysis of the expression profiles of DLBCL samples in the GEO database was performed. Cox regression and LASSO regression analysis were used to determine NK cell-related genes associated with patient's prognosis. Based on these genes, a risk assessment model was constructed to predict the prognosis of patients and the effectiveness of treatment. Finally, qRT-PCR was used to verify the expression of gene tags in clinical samples. RESULTS We identified seven prognosis-related NK cell-related genes (MAP2K1, PRKCB, TNFRSF10B, IL18, LAMP1, RASGRP1, and SP110), and DLBCL patients were divided into low- and high-risk groups based on these genes. Survival analysis showed that the prognosis of patients with low-risk group was better. Pathway enrichment analysis showed that the differentially expressed genes between the two risk groups were related to immune response pathways. Compared with the high-risk group, the low-risk group had higher infiltration of immune cells in tumor tissues. Besides, compared with high-risk group, low-risk patients by immunotherapy or other commonly used anti-tumor drugs might have better efficacy after treatment. In addition, qRT-PCR showed that the expression of risk genes including TNFRSF10B, IL18 and LAMP1 were significantly increased in most DLBCL samples compared to control samples, while the expression of protective genes including MAP2K1, PRKCB, RASGRP1 and SP110 were significantly decreased. CONCLUSION The NK cell-related gene signatures were proved to be a reliable indicator of the success of immunotherapy in patients with DLBCL, thus providing a unique evaluation method.
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Affiliation(s)
- Wei Xiao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, No. 628 Zhenyuan Road, Guangming District, Shenzhen 518107, Guangdong Province, China
| | - Kuai Yu
- Department of Blood Transfusion, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang 330209, Jiangxi Province, China; Key Laboratory of Jiangxi Province for Transfusion Medicine, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Nanchang 330209, Jiangxi Province, China
| | - Xuefei Deng
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, No. 628 Zhenyuan Road, Guangming District, Shenzhen 518107, Guangdong Province, China
| | - Yunxin Zeng
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, No. 628 Zhenyuan Road, Guangming District, Shenzhen 518107, Guangdong Province, China.
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Gong Y, Germeraad WTV, Zhang X, Wu N, Li B, Janssen L, He Z, Gijbels MJJ, Wu B, Gijsbers BLMG, Olieslagers TI, Bos GMJ, Zheng L, Klein Wolterink RGJ. NKG2A genetic deletion promotes human primary NK cell anti-tumor responses better than an anti-NKG2A monoclonal antibody. Mol Ther 2024; 32:2711-2727. [PMID: 38943249 DOI: 10.1016/j.ymthe.2024.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/04/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024] Open
Abstract
Natural killer (NK) cells eliminate infected or cancer cells via their cytotoxic capacity. NKG2A is an inhibitory receptor on NK cells and cancer cells often overexpress its ligand HLA-E to evade NK cell surveillance. Given the successes of immune checkpoint blockade in cancer therapy, NKG2A is an interesting novel target. However, anti-NKG2A antibodies have shown limited clinical response. In the pursuit of enhancing NK cell-mediated anti-tumor responses, we devised a Cas9-based strategy to delete KLRC1, encoding NKG2A, in human primary NK cells. Our approach involved electroporation of KLRC1-targeting Cas9 ribonucleoprotein resulting in effective ablation of NKG2A expression. Compared with anti-NKG2A antibody blockade, NKG2AKO NK cells exhibited enhanced activation, reduced suppressive signaling, and elevated expression of key transcription factors. NKG2AKO NK cells overcame inhibition from HLA-E, significantly boosting NK cell activity against solid and hematologic cancer cells. We validated this efficacy across multiple cell lines, a xenograft mouse model, and primary human leukemic cells. Combining NKG2A knockout with antibody coating of tumor cells further enhanced cytotoxicity through ADCC. Thus, we provide a comprehensive comparison of inhibition of the NKG2A pathway using genetic ablation and antibodies and provide novel insight in the observed differences in molecular mechanisms, which can be translated to enhance adoptive NK cell immunotherapy.
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Affiliation(s)
- Ying Gong
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China; Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands
| | - Wilfred T V Germeraad
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands; CiMaas BV, 6202 AZ Maastricht, the Netherlands
| | - Xulin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Vision Science, Guangzhou 510000, China
| | - Nisha Wu
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Bo Li
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China
| | - Lynn Janssen
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands
| | - Zongzhong He
- Department of Transfusion Medicine of General Hospital of Southern Theatre Command, Guangzhou 510515, P.R. China
| | - Marion J J Gijbels
- GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands; Department of Pathology, Maastricht University Medical Center+, Maastricht, the Netherlands; Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam UMC, 1081 HV Amsterdam, the Netherlands
| | - Bodeng Wu
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China
| | - Birgit L M G Gijsbers
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands
| | - Timo I Olieslagers
- GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands; Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, 6202 AZ Maastricht, the Netherlands
| | - Gerard M J Bos
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands; CiMaas BV, 6202 AZ Maastricht, the Netherlands
| | - Lei Zheng
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China.
| | - Roel G J Klein Wolterink
- Department of Internal Medicine, Division of Hematology, Maastricht University Medical Center+, 6227 HX Maastricht, the Netherlands; GROW - Research Institute for Oncology & Reproduction, Maastricht University, 6202 AZ Maastricht, the Netherlands.
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Wang YH, Hagiwara S, Kazama H, Iizuka Y, Tanaka N, Tanaka J. Elotuzumab Enhances CD16-Independent NK Cell-Mediated Cytotoxicity against Myeloma Cells by Upregulating Several NK Cell-Enhancing Genes. J Immunol Res 2024; 2024:1429879. [PMID: 38444839 PMCID: PMC10914431 DOI: 10.1155/2024/1429879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Multiple myeloma (MM) is an intractable hematological malignancy caused by abnormalities in plasma cells. Combination therapy using antibodies and natural killer (NK) effectors, which are innate immune cells with safe and potent antitumor activity, is a promising approach for cancer immunotherapy and can enhance antitumor effects. Elotuzumab (Elo) is an immune-stimulatory antibody that targets the signaling lymphocytic activation molecule family 7 (SLAMF7) expressed on the surface of MM and NK cells. We confirmed that Elo strongly promoted NK cell-mediated antibody-dependent cellular cytotoxicity (ADCC) against SLAMF7-positive MM cells in a CD16-dependent NK cell line, and also activated expanded NK cells derived from peripheral blood mononuclear cells of healthy donors and patients with MM in the present study. However, the antitumor effects and genes involved in the direct promotion of NK cell-mediated activation using Elo in CD16-independent NK cells are not clearly known. In this study, we demonstrated that Elo pretreatment significantly enhanced CD16-independent NK cell-mediated cytotoxicity in both SLAMF7-positive MM.1S and SLAMF7-negative K562, U266, and RPMI 8226 tumor cells. Upon direct simulation of CD16-independent NK cells with Elo, increased levels of CD107a degranulation and IFN-γ secretion were observed along with the upregulation of granzyme B, TNF-α, and IL-1α gene expression. The enhanced NK cell function could also be attributed to the increased expression of the transcription factors T-BET and EOMES. Furthermore, the augmentation of the antitumor effects of CD16-independent NK cells upon pretreatment with Elo enhanced the expression of CRTAM, TNFRSF9, EAT-2, and FOXP3 genes and reduced the expression of HSPA6. Our results suggest that Elo directly promotes the cytotoxic function of CD16-independent NK cells against target cells, which is associated with the upregulation of the expression of several NK cell-enhancing genes.
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Affiliation(s)
- Yan-Hua Wang
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
| | - Shotaro Hagiwara
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
| | - Hiroshi Kazama
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
- Department of Medicine, Tokyo Women's Medical University, Adachi Medical Center, 4-33-1, Kohoku, Adachi-Ku, Tokyo 123-8558, Japan
| | - Yuki Iizuka
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
| | - Norina Tanaka
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
| | - Junji Tanaka
- Department of Hematology, Tokyo Women's Medical University, 8-1, Kawada-Cho, Shinjuku-Ku, Tokyo 162-8666, Japan
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Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity 2023; 56:2816-2835.e13. [PMID: 38091953 DOI: 10.1016/j.immuni.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.
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Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Sara Gandolfi
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hanna Duàn
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Khalid Saeed
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Petra Nygren
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jonas Bouhlal
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Anna Näätänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Hannunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Pauliina Rumm
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Essi Laajala
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Merja Heinäniemi
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Hollmén
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
| | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Dean A Lee
- Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
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Liu Z, Ding M, Qiu P, Pan K, Guo Q. Natural killer cell-related prognostic risk model predicts prognosis and treatment outcomes in triple-negative breast cancer. Front Immunol 2023; 14:1200282. [PMID: 37520534 PMCID: PMC10373504 DOI: 10.3389/fimmu.2023.1200282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Natural killer (NK) cells are crucial to the emergence, identification, and prognosis of cancers. The roles of NK cell-related genes in the tumor immune microenvironment (TIME) and immunotherapy treatment are unclear. Triple-negative breast cancer (TNBC) is a highly aggressive malignant tumor. Hence, this study was conducted to develop a reliable risk model related to NK cells and provide a novel system for predicting the prognosis of TNBC. Methods NK cell-related genes were collected from previous studies. Based on TCGA and GEO database, univariate and LASSO cox regression analysis were used to establish the NK cell-related gene signature. The patients with TNBC were separated to high-risk and low-risk groups. After that, survival analysis was conducted and the responses to immunotherapies were evaluated on the basis of the signature. Moreover, the drug sensitivity of some traditional chemotherapeutic drugs was assessed by using the "oncoPredict" R package. In addition, the expression levels of the genes involved in the signature were validated by using qRT-PCR in TNBC cell lines. Results The patients with TNBC were divided into high- and low-risk groups according to the median risk score of the 5-NK cell-related gene signature. The low-risk group was associated with a better clinical outcome. Besides, the differentially expressed genes between the different risk groups were enriched in the biological activities associated with immunity. The tumor immune cells were found to be highly infiltrated in the low-risk groups. In accordance with the TIDE score and immune checkpoint-related gene expression analysis, TNBC patients in the low-risk groups were suggested to have better responses to immunotherapies. Eventually, some classical anti-tumor drugs were shown to be less effective in high-risk groups than in low-risk groups. Conclusion The 5-NK cell-related gene signature exhibit outstanding predictive performance and provide fresh viewpoints for evaluating the success of immunotherapy. It will provide new insights to achieve precision and integrated treatment for TNBC in the future.
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Affiliation(s)
- Zundong Liu
- Stem Cell Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Mingji Ding
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Pengjun Qiu
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Kelun Pan
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Qiaonan Guo
- Department of Breast and Thyroid Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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6
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Depierreux DM, Smith GL, Ferguson BJ. Transcriptional reprogramming of natural killer cells by vaccinia virus shows both distinct and conserved features with mCMV. Front Immunol 2023; 14:1093381. [PMID: 36911702 PMCID: PMC9995584 DOI: 10.3389/fimmu.2023.1093381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/09/2023] [Indexed: 02/25/2023] Open
Abstract
Natural killer (NK) cells have an established role in controlling poxvirus infection and there is a growing interest to exploit their capabilities in the context of poxvirus-based oncolytic therapy and vaccination. How NK cells respond to poxvirus-infected cells to become activated is not well established. To address this knowledge gap, we studied the NK cell response to vaccinia virus (VACV) in vivo, using a systemic infection murine model. We found broad alterations in NK cells transcriptional activity in VACV-infected mice, consistent with both direct target cell recognition and cytokine exposure. There were also alterations in the expression levels of specific NK surface receptors (NKRs), including the Ly49 family and SLAM receptors, as well as upregulation of memory-associated NK markers. Despite the latter observation, adoptive transfer of VACV-expercienced NK populations did not confer protection from infection. Comparison with the NK cell response to murine cytomegalovirus (MCMV) infection highlighted common features, but also distinct NK transcriptional programmes initiated by VACV. Finally, there was a clear overlap between the NK transcriptional response in humans vaccinated with an attenuated VACV, modified vaccinia Ankara (MVA), demonstrating conservation between the NK response in these different host species. Overall, this study provides new data about NK cell activation, function, and homeostasis during VACV infection, and may have implication for the design of VACV-based therapeutics.
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Shembrey C, Foroutan M, Hollande F. A new natural killer cell-specific gene signature predicting recurrence in colorectal cancer patients. Front Immunol 2023; 13:1011247. [PMID: 36685584 PMCID: PMC9853446 DOI: 10.3389/fimmu.2022.1011247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023] Open
Abstract
The protective role of Natural Killer (NK) cell tumour immunosurveillance has long been recognised in colorectal cancer (CRC). However, as most patients show limited intra-tumoral NK cell infiltration, improving our ability to identify those with high NK cell activity might aid in dissecting the molecular features which underlie NK cell sensitivity. Here, a novel CRC-specific NK cell gene signature that infers NK cell load in primary tissue samples was derived and validated in multiple patient CRC cohorts. In contrast with other NK cell gene signatures that have several overlapping genes across different immune cell types, our NK cell signature has been extensively refined to be specific for CRC-infiltrating NK cells. The specificity of the signature is substantiated in tumour-infiltrating NK cells from primary CRC tumours at the single cell level, and the signature includes genes representative of NK cells of different maturation states, activation status and anatomical origin. Our signature also accurately discriminates murine NK cells, demonstrating the applicability of this geneset when mining datasets generated from preclinical studies. Differential gene expression analysis revealed tumour-intrinsic features associated with NK cell inclusion versus exclusion in CRC patients, with those tumours with predicted high NK activity showing strong evidence of enhanced chemotactic and cytotoxic transcriptional programs. Furthermore, survival modelling indicated that NK signature expression is associated with improved survival outcomes in CRC patients. Thus, scoring CRC samples with this refined NK cell signature might aid in identifying patients with high NK cell activity who could be prime candidates for NK cell directed immunotherapies.
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Affiliation(s)
- Carolyn Shembrey
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Momeneh Foroutan
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Frédéric Hollande
- Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
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Kristensen AB, Wragg KM, Vanderven HA, Lee WS, Silvers J, Kent HE, Grant MD, Kelleher AD, Juno JA, Kent SJ, Parsons MS. Phenotypic and functional characteristics of highly differentiated CD57+NKG2C+ NK cells in HIV-1-infected individuals. Clin Exp Immunol 2022; 210:163-174. [PMID: 36053502 PMCID: PMC9750827 DOI: 10.1093/cei/uxac082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/07/2022] [Accepted: 09/01/2022] [Indexed: 01/24/2023] Open
Abstract
Natural killer (NK) cells are important anti-viral effector cells. The function and phenotype of the NK cells that constitute an individual's NK cell repertoire can be influenced by ongoing or previous viral infections. Indeed, infection with human cytomegalovirus (HCMV) drives the expansion of a highly differentiated NK cell population characterized by expression of CD57 and the activating NKG2C receptor. This NK cell population has also been noted to occur in HIV-1-infected individuals. We evaluated the NK cells of HIV-1-infected and HIV-1-uninfected individuals to determine the relative frequency of highly differentiated CD57+NKG2C+ NK cells and characterize these cells for their receptor expression and responsiveness to diverse stimuli. Highly differentiated CD57+NKG2C+ NK cells occurred at higher frequencies in HCMV-infected donors relative to HCMV-uninfected donors and were dramatically expanded in HIV-1/HCMV co-infected donors. The expanded CD57+NKG2C+ NK cell population in HIV-1-infected donors remained stable following antiretroviral therapy. CD57+NKG2C+ NK cells derived from HIV-1-infected individuals were robustly activated by antibody-dependent stimuli that contained anti-HIV-1 antibodies or therapeutic anti-CD20 antibody, and these NK cells mediated cytolysis through NKG2C. Lastly, CD57+NKG2C+ NK cells from HIV-1-infected donors were characterized by reduced expression of the inhibitory NKG2A receptor. The abundance of highly functional CD57+NKG2C+ NK cells in HIV-1-infected individuals raises the possibility that these NK cells could play a role in HIV-1 pathogenesis or serve as effector cells for therapeutic/cure strategies.
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Affiliation(s)
- Anne B Kristensen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathleen M Wragg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hillary A Vanderven
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Biomedicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, Queensland, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Julie Silvers
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Helen E Kent
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Michael D Grant
- Immunology and Infectious Diseases Program, Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Anthony D Kelleher
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Victoria, Australia
| | - Matthew S Parsons
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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9
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Romero-Martín L, Duran-Castells C, Olivella M, Rosás-Umbert M, Ruiz-Riol M, Sanchez J, Hartigan-O Connor D, Mothe B, Olvera À, Brander C. Disruption of the HLA-E/NKG2X axis is associated with uncontrolled HIV infections. Front Immunol 2022; 13:1027855. [PMID: 36466823 PMCID: PMC9716355 DOI: 10.3389/fimmu.2022.1027855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 09/28/2023] Open
Abstract
The contribution of the HLA-E/NKG2X axis in NK-mediated control of HIV infection remains unclear. We have studied the relationship between HLA-E expression and phenotypical as well as functional characteristics of NK cells, in the context of chronic HIV infection and in an in vitro model of acute infection. High viremia in HIV+ individuals was related to increased HLA-E expression, and changes in NK subpopulations, especially a reduction of the CD56bright as well as an increase in adaptive NK subpopulation. Uncontrolled HIV infection was also characterized by a reversion of the NKG2A/NKG2C expression ratio and a loss of positive and negative regulation of NK mediated by HLA-E. This was reflected in a lower cytotoxic, degranulation and cytokine production capacity, especially in CD56bright and adaptive NK. In line with these results, HLA-E expression showed a positive correlation with viral growth inhibition in an in vitro model of acute infection at day 7, which was lost after 14 days of culture. Using HLA-E expressing K562 cells, we determined that only one out of 11 described HIV-derived HLA-E epitopes increased HLA-E surface stability. In spite of that, eight of the 11 epitopes were capable of increasing degranulation and three drove differences in NK-cell mediated cell lysis or cytokine secretion. In conclusion, our results indicate that HLA-E molecules presenting HIV-derived epitopes may sensitize target cells for NK lysis in early HIV infection. However, prolonged exposure to elevated HLA-E expression levels in vivo may lead to NK cell dysfunction and reduced viral control In chronic infection.
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Affiliation(s)
- Luis Romero-Martín
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Spain
| | - Clara Duran-Castells
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- Universitat Autonoma de Barcelona (UAB), Barcelona, Spain
| | - Mireia Olivella
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Míriam Rosás-Umbert
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- CIBERINFEC, Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Dennis Hartigan-O Connor
- California National Primate Research Center and Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Àlex Olvera
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- CIBERINFEC, Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III, Madrid, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- CIBERINFEC, Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III, Madrid, Spain
- ICREA, Barcelona, Spain
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10
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Mazouz S, Salinas E, Bédard N, Filali A, Khedr O, Swadling L, Abdel-Hakeem MS, Siddique A, Barnes E, Bruneau J, Grakoui A, Shoukry NH. Differential immune transcriptomic profiles between vaccinated and resolved HCV reinfected subjects. PLoS Pathog 2022; 18:e1010968. [PMID: 36378682 PMCID: PMC9707775 DOI: 10.1371/journal.ppat.1010968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/29/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Successive episodes of hepatitis C virus (HCV) infection represent a unique natural rechallenge experiment to define correlates of long-term protective immunity and inform vaccine development. We applied a systems immunology approach to characterize longitudinal changes in the peripheral blood transcriptomic signatures in eight subjects who spontaneously resolved two successive HCV infections. Furthermore, we compared these signatures with those induced by an HCV T cell-based vaccine regimen. We identified a plasma cell transcriptomic signature during early acute HCV reinfection. This signature was absent in primary infection and following HCV vaccine boost. Spontaneous resolution of HCV reinfection was associated with rapid expansion of glycoprotein E2-specifc memory B cells in three subjects and transient increase in E2-specific neutralizing antibodies in six subjects. Concurrently, there was an increase in the breadth and magnitude of HCV-specific T cells in 7 out of 8 subjects. These results suggest a cooperative role for both antibodies and T cells in clearance of HCV reinfection and support the development of next generation HCV vaccines targeting these two arms of the immune system.
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Affiliation(s)
- Sabrina Mazouz
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Eduardo Salinas
- Emory University School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Emory National Primate Research Center, Atlanta, Georgia, United States of America
| | - Nathalie Bédard
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Ali Filali
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Omar Khedr
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mohamed S. Abdel-Hakeem
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Asiyah Siddique
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Julie Bruneau
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de médecine familiale et de médecine d’urgence, Université de Montréal, Montréal, Québec, Canada
| | - Arash Grakoui
- Emory University School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Emory National Primate Research Center, Atlanta, Georgia, United States of America
| | - Naglaa H. Shoukry
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Département de médecine, Université de Montréal, Montréal, Québec, Canada
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11
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Pace M, Ogbe A, Hurst J, Robinson N, Meyerowitz J, Olejniczak N, Thornhill JP, Jones M, Waters A, Lwanga J, Kuldanek K, Hall R, Zacharopoulou P, Martin GE, Brown H, Nwokolo N, Peppa D, Fox J, Fidler S, Frater J. Impact of antiretroviral therapy in primary HIV infection on natural killer cell function and the association with viral rebound and HIV DNA following treatment interruption. Front Immunol 2022; 13:878743. [PMID: 36110857 PMCID: PMC9468877 DOI: 10.3389/fimmu.2022.878743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Natural Killer (NK) cells play a key role in controlling HIV replication, with potential downstream impact on the size of the HIV reservoir and likelihood of viral rebound after antiretroviral therapy (ART) cessation. It is therefore important to understand how primary HIV infection (PHI) disrupts NK cell function, and how these functions are restored by early ART. We examined the impact of commencing ART during PHI on phenotypic and functional NK cell markers at treatment initiation (baseline), 3 months, 1 year, and 2 years in seven well-characterised participants in comparison to HIV seronegative volunteers. We then examined how those NK cell properties differentially impacted by ART related to time to viral rebound and HIV DNA levels in 44 individuals from the SPARTAC trial who stopped ART after 48 weeks treatment, started during PHI. NK cell markers that were significantly different between the seven people with HIV (PWH) treated for 2 years and HIV uninfected individuals included NKG2C levels in CD56dim NK cells, Tim-3 expression in CD56bright NK cells, IFN-γ expressed by CD56dim NK cells after IL-12/IL-18 stimulation and the fraction of Eomes-/T-bet+ in CD56dim and CD56bright NK cells. When exploring time to viral rebound after stopping ART among the 44 SPARTAC participants, no single NK phenotypic marker correlated with control. Higher levels of IL-12/IL-18 mediated NK cell degranulation at baseline were associated with longer times to viral rebound after treatment interruption (P=0.028). Additionally, we found higher fractions of CD56dim NK cells in individuals with lower levels of HIV DNA (P=0.048). NKG2A and NKp30 levels in CD56neg NK cells were higher in patients with lower HIV DNA levels (p=0.00174, r=-0.49 and p=0.03, r= -0.327, respectively) while CD27 levels were higher in those with higher levels of HIV DNA (p=0.026). These data show NK cell functions are heterogeneously impacted by HIV infection with a mixed picture of resolution on ART, and that while NK cells may affect HIV DNA levels and time to viral rebound, no single NK cell marker defined delayed viral rebound.
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Affiliation(s)
- Matthew Pace
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jacob Hurst
- Etcembly Ltd, Harwell Campus, Didcot, United Kingdom
| | - Nicola Robinson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jodi Meyerowitz
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Natalia Olejniczak
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - John P. Thornhill
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mathew Jones
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anele Waters
- Department of Infection, Guys and St Thomas’ National Health Service (NHS) Trust, London, United Kingdom
| | - Julianne Lwanga
- Department of Infection, Guys and St Thomas’ National Health Service (NHS) Trust, London, United Kingdom
| | - Kristen Kuldanek
- Department of HIV Medicine, St Mary’s Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | - Rebecca Hall
- Department of HIV Medicine, St Mary’s Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
| | | | - Genevieve E. Martin
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Helen Brown
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nneka Nwokolo
- Department of HIV/GUM, Chelsea and Westminster Hospital, London, United Kingdom
| | - Dimitra Peppa
- Division of Infection and Immunity, University College, London, United Kingdom
| | - Julie Fox
- Department of Infection, Guys and St Thomas’ National Health Service (NHS) Trust, London, United Kingdom
| | - Sarah Fidler
- Department of HIV Medicine, St Mary’s Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London, United Kingdom
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- National Institute for Health and Care Research (NIHR) Imperial College Biomedical Research Centre, London, United Kingdom
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom
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12
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Song P, Li W, Guo L, Ying J, Gao S, He J. Identification and Validation of a Novel Signature Based on NK Cell Marker Genes to Predict Prognosis and Immunotherapy Response in Lung Adenocarcinoma by Integrated Analysis of Single-Cell and Bulk RNA-Sequencing. Front Immunol 2022; 13:850745. [PMID: 35757748 PMCID: PMC9231585 DOI: 10.3389/fimmu.2022.850745] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Natural killer (NK) cells, the effectors of the innate immune system, have a remarkable influence on cancer prognosis and immunotherapy. In this study, a total of 1,816 samples from nine independent cohorts in public datasets were enrolled. We first conducted a comprehensive analysis of single-cell RNA-sequencing data of lung adenocarcinoma (LUAD) from the Gene Expression Omnibus (GEO) database and determined 189 NK cell marker genes. Subsequently, we developed a seven-gene prognostic signature based on NK cell marker genes in the TCGA LUAD cohort, which stratified patients into high-risk and low-risk groups. The predictive power of the signature was well verified in different clinical subgroups and GEO cohorts. With a multivariate analysis, the signature was identified as an independent prognostic factor. Low-risk patients had higher immune cell infiltration states, especially CD8+ T cells and follicular helper T cells. There existed a negative association between inflammatory activities and risk score, and the richness and diversity of the T-cell receptor (TCR) repertoire was higher in the low-risk groups. Importantly, analysis of an independent immunotherapy cohort (IMvigor210) revealed that low-risk patients had better immunotherapy responses and prognosis than high-risk patients. Collectively, our study developed a novel signature based on NK cell marker genes, which had a potent capability to predict the prognosis and immunotherapy response of LUAD patients.
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Affiliation(s)
- Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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13
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Sun Y, Zhou J, Jiang Y. Negative Regulation and Protective Function of Natural Killer Cells in HIV Infection: Two Sides of a Coin. Front Immunol 2022; 13:842831. [PMID: 35320945 PMCID: PMC8936085 DOI: 10.3389/fimmu.2022.842831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
Natural killer (NK) cells play an important immunologic role, targeting tumors and virus-infected cells; however, NK cells do not impede the progression of human immunodeficiency virus (HIV) infection. In HIV infection, NK cells exhibit impaired functions and negatively regulate other immune cell responses, although NK cells can kill HIV-infected cells and thereby suppress HIV replication. Considerable recent research has emerged regarding NK cells in the areas of immune checkpoints, negative regulation, antibody-dependent cell-mediated cytotoxicity and HIV reservoirs during HIV infection; however, no overall summary of these factors is available. This review focuses on several important aspects of NK cells in relation to HIV infection, including changes in NK cell count, subpopulations, and immune checkpoints, as well as abnormalities in NK cell functions and NK cell negative regulation. The protective function of NK cells in inhibiting HIV replication to reduce the viral reservoir and approaches for enhancing NK cell functions are also summarized.
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14
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Understanding natural killer cell biology from a single cell perspective. Cell Immunol 2022; 373:104497. [DOI: 10.1016/j.cellimm.2022.104497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/26/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022]
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15
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Premeaux TA, Moser CB, McKhann A, Hoenigl M, Yeung ST, Pang APS, Corley MJ, Lederman MM, Landay AL, Gianella S, Ndhlovu LC. Monitoring Circulating Immune Checkpoint Proteins as Predictors of Non-AIDS Morbid Events in People with HIV Initiating Antiretroviral Therapy. Open Forum Infect Dis 2022; 9:ofab570. [PMID: 35146038 PMCID: PMC8826032 DOI: 10.1093/ofid/ofab570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Although cell surface immune checkpoint proteins (ICPs) such as PD-1 expressed on T cells are associated with T-cell exhaustion, HIV disease progression, and AIDS events, they have shown limited utility in predicting non-AIDS morbidity. Given that ICPs also exist in soluble forms and are elevated in ART-treated HIV infection, we tested the hypothesis that soluble ICPs may be predictive of non-AIDS events in adults initiating ART. Methods Utilizing a nested case–control study from the AIDS Clinical Trials Group ALLRT cohort, we measured plasma levels of 15 soluble inhibitory and activating ICPs by Luminex. Participants (134 cases, 292 matched controls) were evaluated pre-ART, a year post-ART, and immediately preceding a non-AIDS event, which included myocardial infarction (MI)/stroke, malignancy, serious bacterial infection, and nonaccidental death. Results Conditional logistic regression analysis determined that higher levels of soluble CD27 were associated with increased risk of non-AIDS events at all time points. Higher levels of CD40 at baseline and pre-event and CD80 at pre-event were associated with increased risk of non-AIDS events. Examining specific non-AIDS events, multiple ICPs were associated with malignancy at baseline and pre-event, whereas only higher CD27 levels were associated with increased risk of MI/stroke at year 1 and pre-event. Conclusions While select soluble ICPs were associated with non-AIDS events, CD27 emerged as a consistent marker irrespective of ART. Our data may offer guidance on new targets for early clinical monitoring in people with HIV who remain at greater risk of specific non-AIDS events.
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Affiliation(s)
- Thomas A Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carlee B Moser
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ashley McKhann
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Stephen T Yeung
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alina P S Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael M Lederman
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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16
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Rascle P, Jacquelin B, Petitdemange C, Contreras V, Planchais C, Lazzerini M, Dereuddre-Bosquet N, Le Grand R, Mouquet H, Huot N, Müller-Trutwin M. NK-B cell cross talk induces CXCR5 expression on natural killer cells. iScience 2021; 24:103109. [PMID: 34622162 PMCID: PMC8479784 DOI: 10.1016/j.isci.2021.103109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023] Open
Abstract
B cell follicles (BCFs) in lymph nodes (LNs) are generally exempt of CD8+ T and NK cells. African green monkeys (AGMs), a natural host of simian immunodeficiency virus (SIV), display NK cell-mediated viral control in BCF. NK cell migration into BCF in chronically SIVagm-infected AGM is associated with CXCR5+ NK cells. We aimed to identify the mechanism leading to CXCR5 expression on NK cells. We show that CXCR5+ NK cells in LN were induced following SIVagm infection. CXCR5+ NK cells accumulated preferentially in BCF with proliferating B cells. Autologous NK-B cell co-cultures in transwell chambers induced CXCR5+ NK cells. Transcriptome analysis of CXCR5+ NK cells revealed expression of bcl6 and IL6R. IL-6 induced CXCR5 on AGM and human NK cells. IL6 mRNA was detected in LN at higher levels during SIVagm than SIVmac infection and often produced by plasma cells. Our study reveals a mechanism of B cell-dependent NK cell regulation. IL-6 can induce CXCR5 on NK cells CXCR5+ NK cells expressed high levels of bcl6 and IL6R More IL-6+ plasmablast/plasma cells in lymph nodes in SIVagm than SIVmac infection B cells participate in the regulation of NK cell migration into BCF
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Affiliation(s)
- Philippe Rascle
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Béatrice Jacquelin
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Caroline Petitdemange
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Vanessa Contreras
- CEA, Université Paris-Saclay, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, Paris, France
| | - Cyril Planchais
- Institut Pasteur, Laboratory of Humoral Immunology, Paris, France.,INSERM U1222, Paris, France
| | - Marie Lazzerini
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nathalie Dereuddre-Bosquet
- CEA, Université Paris-Saclay, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, Paris, France
| | - Roger Le Grand
- CEA, Université Paris-Saclay, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Laboratory of Humoral Immunology, Paris, France.,INSERM U1222, Paris, France
| | - Nicolas Huot
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Michaela Müller-Trutwin
- Institut Pasteur, HIV Inflammation and Persistence Unit, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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17
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Woods E, Zaiatz-Bittencourt V, Bannan C, Bergin C, Finlay DK, Hoffmann M, Brown A, Turner B, Makvandi-Nejad S, Vassilev V, Capone S, Folgori A, Hanke T, Barnes E, Dorrell L, Gardiner CM. Specific human cytomegalovirus signature detected in NK cell metabolic changes post vaccination. NPJ Vaccines 2021; 6:117. [PMID: 34584101 PMCID: PMC8478984 DOI: 10.1038/s41541-021-00381-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
Effective vaccines for human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) remain a significant challenge for these infectious diseases. Given that the innate immune response is key to controlling the scale and nature of developing adaptive immune responses, targeting natural killer (NK) cells that can promote a T-helper type 1 (Th1)-type immune response through the production of interferon-γ (IFNγ) remains an untapped strategic target for improved vaccination approaches. Here, we investigate metabolic and functional responses of NK cells to simian adenovirus prime and MVA boost vaccination in a cohort of healthy volunteers receiving a dual HCV-HIV-1 vaccine. Early and late timepoints demonstrated metabolic changes that contributed to the sustained proliferation of all NK cells. However, a strong impact of human cytomegalovirus (HCMV) on some metabolic and functional responses in NK cells was observed in HCMV seropositive participants. These changes were not restricted to molecularly defined adaptive NK cells; indeed, canonical NK cells that produced most IFNγ in response to vaccination were equally impacted in individuals with latent HCMV. In summary, NK cells undergo metabolic changes in response to vaccination, and understanding these in the context of HCMV is an important step towards rational vaccine design against a range of human viral pathogens.
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Affiliation(s)
- Elena Woods
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Vanessa Zaiatz-Bittencourt
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | | | | | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
- School of Pharmacy, Trinity College, Dublin 2, Ireland
| | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Internal Medicine, Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital Olten, Olten, Switzerland
| | - Anthony Brown
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bethany Turner
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Clair M Gardiner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland.
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18
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Vázquez-Jiménez A, Avila-Ponce De León UE, Matadamas-Guzman M, Muciño-Olmos EA, Martínez-López YE, Escobedo-Tapia T, Resendis-Antonio O. On Deep Landscape Exploration of COVID-19 Patients Cells and Severity Markers. Front Immunol 2021; 12:705646. [PMID: 34603282 PMCID: PMC8481922 DOI: 10.3389/fimmu.2021.705646] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is a disease with a spectrum of clinical responses ranging from moderate to critical. To study and control its effects, a large number of researchers are focused on two substantial aims. On the one hand, the discovery of diverse biomarkers to classify and potentially anticipate the disease severity of patients. These biomarkers could serve as a medical criterion to prioritize attention to those patients with higher prone to severe responses. On the other hand, understanding how the immune system orchestrates its responses in this spectrum of disease severities is a fundamental issue required to design new and optimized therapeutic strategies. In this work, using single-cell RNAseq of bronchoalveolar lavage fluid of nine patients with COVID-19 and three healthy controls, we contribute to both aspects. First, we presented computational supervised machine-learning models with high accuracy in classifying the disease severity (moderate and severe) in patients with COVID-19 starting from single-cell data from bronchoalveolar lavage fluid. Second, we identified regulatory mechanisms from the heterogeneous cell populations in the lungs microenvironment that correlated with different clinical responses. Given the results, patients with moderate COVID-19 symptoms showed an activation/inactivation profile for their analyzed cells leading to a sequential and innocuous immune response. In comparison, severe patients might be promoting cytotoxic and pro-inflammatory responses in a systemic fashion involving epithelial and immune cells without the possibility to develop viral clearance and immune memory. Consequently, we present an in-depth landscape analysis of how transcriptional factors and pathways from these heterogeneous populations can regulate their expression to promote or restrain an effective immune response directly linked to the patients prognosis.
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Affiliation(s)
- Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Ugo Enrique Avila-Ponce De León
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biológicas, UNAM, Mexico City, Mexico
| | - Meztli Matadamas-Guzman
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, UNAM, Mexico City, Mexico
| | - Erick Andrés Muciño-Olmos
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, UNAM, Mexico City, Mexico
| | - Yoscelina E. Martínez-López
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado en Ciencias Médicas y de la Salud, UNAM, Mexico City, Mexico
| | - Thelma Escobedo-Tapia
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, UNAM, Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, UNAM, Mexico City, Mexico
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19
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Devalraju KP, Neela VSK, Krovvidi SS, Vankayalapati R, Valluri VL. Defective expansion and function of memory like natural killer cells in HIV+ individuals with latent tuberculosis infection. PLoS One 2021; 16:e0257185. [PMID: 34516566 PMCID: PMC8437280 DOI: 10.1371/journal.pone.0257185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 08/25/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose Tuberculosis (TB) is the leading cause of infectious disease related mortality, and only 10% of the infected individuals develop active disease. The likelihood of progression of latent tuberculosis infection (LTBI) to active TB disease is high in HIV infected individuals. Identification of HIV+ individuals at risk would allow treating targeted population, facilitating completion of therapy for LTBI and prevention of TB development. NK cells have an important role in T cell independent immunity against TB, but the exact role of NK cell subsets in LTBI and HIV is not well characterized. Methods In this study, we compared the expansion and function of memory like NK cells from HIV-LTBI+ individuals and treatment naïve HIV+LTBI+ patients in response to Mtb antigens ESAT-6 and CFP-10. Results In freshly isolated PBMCs, percentages of CD3-CD56+ NK cells were similar in HIV+LTBI+ patients and healthy HIV-LTBI+ individuals. However, percentages of CD3-CD56+CD16+ NK cells were higher in healthy HIV-LTBI+ individuals compared to HIV+LTBI+ patients. HIV infection also inhibited the expansion of memory like NK cells, production of IL-32α, IL-15 and IFN-γ in response to Mtb antigens in LTBI+ individuals. Conclusion We studied phenotypic, functional subsets and activation of memory like-NK cells during HIV infection and LTBI. We observed that HIV+LTBI+ patients demonstrated suboptimal NK cell and monocyte interactions in response to Mtb, leading to reduced IL-15, IFN-γ and granzyme B and increased CCL5 production. Our study highlights the effect of HIV and LTBI on modulation of NK cell activity to understand their role in development of interventions to prevent progression to TB in high risk individuals.
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Affiliation(s)
- Kamakshi Prudhula Devalraju
- Immunology and Molecular Biology Division, Blue Peter Public Health and Research Centre, LEPRA Society, Cherlapally, Hyderabad, Telangana, India
| | - Venkata Sanjeev Kumar Neela
- Immunology and Molecular Biology Division, Blue Peter Public Health and Research Centre, LEPRA Society, Cherlapally, Hyderabad, Telangana, India
| | - Siva Sai Krovvidi
- Department of Biotechnology, Sreenidhi Institute of Science and Technology, Yamnampet, Ghatkesar, Hyderabad, Telangana, India
| | - Ramakrishna Vankayalapati
- Department of Pulmonary Immunology, Center for Biomedical Research, The University of Texas Health Center at Tyler, Texas, TX, United States of America
- * E-mail: (VLV); (RV)
| | - Vijaya Lakshmi Valluri
- Immunology and Molecular Biology Division, Blue Peter Public Health and Research Centre, LEPRA Society, Cherlapally, Hyderabad, Telangana, India
- * E-mail: (VLV); (RV)
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20
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Fehér C, Pastor-lbáñez R, Leal L, Plana M, Arnedo M, van den Ham HJ, Andeweg AC, Gruters RA, Díez-Fuertes F, Alcamí J, Aloy P, García F. Association of Transcriptomic Signatures of Inflammatory Response with Viral Control after Dendritic Cell-Based Therapeutic Vaccination in HIV-1 Infected Individuals. Vaccines (Basel) 2021; 9:vaccines9070799. [PMID: 34358215 PMCID: PMC8310264 DOI: 10.3390/vaccines9070799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 12/01/2022] Open
Abstract
Systems vaccinology has seldomly been used in therapeutic HIV-1 vaccine research. Our aim was to identify early gene ‘signatures’ that predicted virus load control after analytical therapy interruption (ATI) in participants of a dendritic cell-based HIV-1 vaccine trial (DCV2). mRNA and miRNA were extracted from frozen post-vaccination PBMC samples; gene expression was determined by microarray method. In gene set enrichment analysis, responders showed an up-regulation of 14 gene sets (TNF-alpha/NFkB pathway, inflammatory response, the complement system, Il6 and Il2 JAK-STAT signaling, among others) and a down-regulation of 7 gene sets (such as E2F targets or interferon alpha response). The expression of genes regulated by three (miR-223-3p, miR-1183 and miR-8063) of the 9 differentially expressed miRNAs was significantly down-regulated in responders. The deregulation of certain gene sets related to inflammatory processes seems fundamental for viral control, and certain miRNAs may be important in fine-tuning these processes.
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Affiliation(s)
- Csaba Fehér
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, 08028 Barcelona, Spain;
- Infectious Diseases Department, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain; (L.L.); (F.D.-F.); (J.A.); (F.G.)
- Correspondence:
| | - Roque Pastor-lbáñez
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-l.); (M.P.); (M.A.)
| | - Lorna Leal
- Infectious Diseases Department, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain; (L.L.); (F.D.-F.); (J.A.); (F.G.)
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-l.); (M.P.); (M.A.)
| | - Montserrat Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-l.); (M.P.); (M.A.)
| | - Mireia Arnedo
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-l.); (M.P.); (M.A.)
| | - Henk-Jan van den Ham
- Department of Viroscience, Erasmus MC, 3000CA Rotterdam, The Netherlands; (H.-J.v.d.H.); (A.C.A.); (R.A.G.)
| | - Arno C. Andeweg
- Department of Viroscience, Erasmus MC, 3000CA Rotterdam, The Netherlands; (H.-J.v.d.H.); (A.C.A.); (R.A.G.)
| | - Rob A. Gruters
- Department of Viroscience, Erasmus MC, 3000CA Rotterdam, The Netherlands; (H.-J.v.d.H.); (A.C.A.); (R.A.G.)
| | - Francisco Díez-Fuertes
- Infectious Diseases Department, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain; (L.L.); (F.D.-F.); (J.A.); (F.G.)
- National Center for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - José Alcamí
- Infectious Diseases Department, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain; (L.L.); (F.D.-F.); (J.A.); (F.G.)
- National Center for Microbiology, Instituto de Salud Carlos III, 28222 Majadahonda, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, 08028 Barcelona, Spain;
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Felipe García
- Infectious Diseases Department, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain; (L.L.); (F.D.-F.); (J.A.); (F.G.)
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (R.P.-l.); (M.P.); (M.A.)
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21
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Pastor-Ibáñez R, Díez-Fuertes F, Sánchez-Palomino S, Alcamí J, Plana M, Torrents D, Leal L, García F. Impact of Transcriptome and Gut Microbiome on the Response of HIV-1 Infected Individuals to a Dendritic Cell-Based HIV Therapeutic Vaccine. Vaccines (Basel) 2021; 9:vaccines9070694. [PMID: 34202658 PMCID: PMC8310021 DOI: 10.3390/vaccines9070694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023] Open
Abstract
Therapeutic vaccines based on dendritic cells offer a good approach to HIV-specific T-cell responses and partial control of the viral load after antiretroviral therapy interruption. The aim of the present study was to identify mRNA expression profiles and to assess the impact of the gut microbiome composition for predicting the viral load control after antiretroviral therapy interruption. We enrolled 29 patients to receive either placebo or a monocyte-derived dendritic cell vaccine. Patients with a decrease in their viral load of >0.5 log10 copies/mL by 12 weeks after antiretroviral therapy interruption were considered responders. In total, 66 genes were considered differentially expressed between responders and non-responders. Enrichment analysis revealed several upregulated pathways involved in the host defense response to a virus via the type I interferon signaling pathway. Regarding the gut microbiota, responders showed enriched levels of Bacteroidetes (p < 0.005) and Verrucomicrobia (p = 0.017), while non-responders were enriched with Tenericutes (p = 0.049) and Actinobacteria (p < 0.005). We also found important differences at the genus level. However, we did not discover any effect of the dendritic cell vaccine on the transcriptome or the gut microbiota. An alternative analysis did characterize that the microbiota from responders were associated with the metabolic production of short-chain fatty acids, which are key metabolites in the regulation of intestinal homeostasis. The evidence now consistently shows that short-chain fatty acid depletion occurs in HIV-infected individuals receiving antiretroviral treatment.
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Affiliation(s)
- Roque Pastor-Ibáñez
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | | | - Sonsoles Sánchez-Palomino
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | - Jose Alcamí
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, Majadahonda, 28222 Madrid, Spain;
| | - Montserrat Plana
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
| | - David Torrents
- Computational Genomics Groups, Barcelona Supercomputing Center (BSC), Plaça d’Eusebi Güell, 1-3, 08034 Barcelona, Spain;
| | - Lorna Leal
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Infectious Diseases—Department, Hospital Clínic, IDIBAPS, University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-932-275-586; Fax: +34-934-514-438
| | - Felipe García
- AIDS Research Group, IDIBAPS, Hospital Clinic, University of Barcelona, 170, 08036 Barcelona, Spain; (R.P.-I.); (S.S.-P.); (J.A.); (M.P.); (F.G.)
- Infectious Diseases—Department, Hospital Clínic, IDIBAPS, University of Barcelona, Villarroel, 170, 08036 Barcelona, Spain
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22
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Herrera-Uribe J, Wiarda JE, Sivasankaran SK, Daharsh L, Liu H, Byrne KA, Smith TPL, Lunney JK, Loving CL, Tuggle CK. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. Front Genet 2021; 12:689406. [PMID: 34249103 PMCID: PMC8261551 DOI: 10.3389/fgene.2021.689406] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023] Open
Abstract
Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B-cell, conventional CD4 and CD8 αβ T-cells, NK cells, and γδ T-cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T-cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Jayne E. Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Immunobiology Graduate Program, Iowa State University, Ames, IA, United States
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States
| | - Sathesh K. Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kristen A. Byrne
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | | | - Joan K. Lunney
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States
| | - Crystal L. Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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23
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Abeynaike S, Paust S. Humanized Mice for the Evaluation of Novel HIV-1 Therapies. Front Immunol 2021; 12:636775. [PMID: 33868262 PMCID: PMC8047330 DOI: 10.3389/fimmu.2021.636775] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
With the discovery of antiretroviral therapy, HIV-1 infection has transitioned into a manageable but chronic illness, which requires lifelong treatment. Nevertheless, complete eradication of the virus has still eluded us. This is partly due to the virus’s ability to remain in a dormant state in tissue reservoirs, ‘hidden’ from the host’s immune system. Also, the high mutation rate of HIV-1 results in escape mutations in response to many therapeutics. Regardless, the development of novel cures for HIV-1 continues to move forward with a range of approaches from immunotherapy to gene editing. However, to evaluate in vivo pathogenesis and the efficacy and safety of therapeutic approaches, a suitable animal model is necessary. To this end, the humanized mouse was developed by McCune in 1988 and has continued to be improved on over the past 30 years. Here, we review the variety of humanized mouse models that have been utilized through the years and describe their specific contribution in translating HIV-1 cure strategies to the clinic.
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Affiliation(s)
- Shawn Abeynaike
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,The Skaggs Graduate Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States
| | - Silke Paust
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,The Skaggs Graduate Program in Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, United States
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24
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Fujimoto M, Kamiyama M, Fuse K, Ryuno H, Odawara T, Furukawa N, Yoshimatsu Y, Watabe T, Prchal-Murphy M, Sexl V, Tahara H, Hayakawa Y, Sato T, Takeda K, Naguro I, Ichijo H. ASK1 suppresses NK cell-mediated intravascular tumor cell clearance in lung metastasis. Cancer Sci 2021; 112:1633-1643. [PMID: 33565179 PMCID: PMC8019214 DOI: 10.1111/cas.14842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor metastasis is the leading cause of death worldwide and involves an extremely complex process composed of multiple steps. Our previous study demonstrated that apoptosis signal‐regulating kinase 1 (ASK1) deficiency in mice attenuates tumor metastasis in an experimental lung metastasis model. However, the steps of tumor metastasis regulated by ASK1 remain unclear. Here, we showed that ASK1 deficiency in mice promotes natural killer (NK) cell‐mediated intravascular tumor cell clearance in the initial hours of metastasis. In response to tumor inoculation, ASK1 deficiency upregulated immune response‐related genes, including interferon‐gamma (IFNγ). We also revealed that NK cells are required for these anti‐metastatic phenotypes. ASK1 deficiency augmented cytokine production chemoattractive to NK cells possibly through induction of the ligand for NKG2D, a key activating receptor of NK cells, leading to further recruitment of NK cells into the lung. These results indicate that ASK1 negatively regulates NK cell‐dependent anti‐tumor immunity and that ASK1‐targeted therapy can provide a new tool for cancer immunotherapy to overcome tumor metastasis.
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Affiliation(s)
- Makoto Fujimoto
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Miki Kamiyama
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kosuke Fuse
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Ryuno
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeru Odawara
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsuki Furukawa
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuhiro Yoshimatsu
- Division of Pharmacology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michaela Prchal-Murphy
- Department of Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine of Vienna, Wien, Austria
| | - Veronika Sexl
- Department of Biomedical Sciences, Institute of Pharmacology and Toxicology, University of Veterinary Medicine of Vienna, Wien, Austria
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Center, Osaka International Cancer Institute, Osaka, Japan.,Project Division of Cancer Biomolecular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Hayakawa
- Division of Pathogenic Biochemistry, Institute of Natural Medicine, University of Toyama, Toyama, Japan
| | - Takehiro Sato
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kohsuke Takeda
- Division of Cell Regulation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Isao Naguro
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hidenori Ichijo
- Laboratory of Cell Signaling, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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25
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Cruz-Pulido D, Boley PA, Ouma WZ, Alhamo MA, Saif LJ, Kenney SP. Comparative Transcriptome Profiling of Human and Pig Intestinal Epithelial Cells after Porcine Deltacoronavirus Infection. Viruses 2021; 13:v13020292. [PMID: 33668405 PMCID: PMC7918119 DOI: 10.3390/v13020292] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 01/16/2023] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging infectious disease of swine with zoonotic potential. Phylogenetic analysis suggests that PDCoV originated recently from a host-switching event between birds and mammals. Little is known about how PDCoV interacts with its differing hosts. Human-derived cell lines are susceptible to PDCoV infection. Herein, we compare the gene expression profiles of an established host swine cells to potential emerging host human cells after infection with PDCoV. Cell lines derived from intestinal lineages were used to reproduce the primary sites of viral infection in the host. Porcine intestinal epithelial cells (IPEC-J2) and human intestinal epithelial cells (HIEC) were infected with PDCoV. RNA-sequencing was performed on total RNA extracted from infected cells. Human cells exhibited a more pronounced response to PDCoV infection in comparison to porcine cells with more differentially expressed genes (DEGs) in human, 7486, in comparison to pig cells, 1134. On the transcriptional level, the adoptive host human cells exhibited more DEGs in response to PDCoV infection in comparison to the primary pig host cells, where different types of cytokines can control PDCoV replication and virus production. Key immune-associated DEGs and signaling pathways are shared between human and pig cells during PDCoV infection. These included genes related to the NF-kappa-B transcription factor family, the interferon (IFN) family, the protein-kinase family, and signaling pathways such as the apoptosis signaling pathway, JAK-STAT signaling pathway, inflammation/cytokine–cytokine receptor signaling pathway. MAP4K4 was unique in up-regulated DEGs in humans in the apoptosis signaling pathway. While similarities exist between human and pig cells in many pathways, our research suggests that the adaptation of PDCoV to the porcine host required the ability to down-regulate many response pathways including the interferon pathway. Our findings provide an important foundation that contributes to an understanding of the mechanisms of PDCoV infection across different hosts. To our knowledge, this is the first report of transcriptome analysis of human cells infected by PDCoV.
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Affiliation(s)
- Diana Cruz-Pulido
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Patricia A. Boley
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | | | - Moyasar A. Alhamo
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Linda J. Saif
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
| | - Scott P. Kenney
- Department of Veterinary Preventive Medicine, Food Animal Health Research Program (FAHRP), Wooster, OH 44691, USA; (D.C.-P.); (P.A.B.); (M.A.A.); (L.J.S.)
- Correspondence: ; Tel.: +1-330-263-3747
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26
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Sugawara S, Manickam C, Reeves K. TRIGGERED: could refocused cell signaling be key to natural killer cell-based HIV immunotherapeutics? AIDS 2021; 35:165-176. [PMID: 33116071 PMCID: PMC7775286 DOI: 10.1097/qad.0000000000002743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Natural killer (NK) cells are one of the critical innate immune effector cells that directly kill tumors and virus-infected cells, and modulate other immune cells including dendritic cells, CD4+ and CD8+ T cells. Signals from activating and inhibitory surface receptors orchestrate the regulatory and cytotoxic functions of NK cells. Although a number of surface receptors are involved, multiple signaling molecules are shared so that NK cell responses are synergistically regulated. Many pathogens and tumors evade NK cell responses by targeting NK cell signaling. Particularly in HIV/simian immunodeficiency virus (SIV) infection, the NK cell repertoire is diminished by changes in subsets of NK cells, expression of activating and inhibitory receptors, and intracellular signaling molecules. However, in-depth studies on intracellular signaling in NK cells in HIV/SIV infections remain limited. Checkpoint blockade and chimeric antigen receptor (CAR)-NK cells have demonstrated enhanced NK cell activities against tumors and viral infections. In addition, targeting intracellular signaling molecules by small molecules could also improve NK cell responses towards HIV/SIV infection in vivo. Therefore, further understanding of NK cell signaling including identification of key signaling molecules is crucial to maximize the efficacy of NK cell-based treatments. Herein, we review the current state of the literature and outline potential future avenues where optimized NK cells could be utilized in HIV-1 cure strategies and other immunotherapeutics in PLWH.
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Affiliation(s)
- Sho Sugawara
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Cordelia Manickam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA
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27
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Wang S, Zhang Q, Hui H, Agrawal K, Karris MAY, Rana TM. An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics. Emerg Microbes Infect 2020; 9:2333-2347. [PMID: 32954948 PMCID: PMC7646563 DOI: 10.1080/22221751.2020.1826361] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4+ and CD8+ T cells and interferon-responsive CD8+ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8+ T cell population expressing KLRG1, TIGIT, and T-betdimEomeshi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8+ T cells demonstrating the contribution of KLRG1+ population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
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Affiliation(s)
- Shaobo Wang
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
| | - Qiong Zhang
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
| | - Hui Hui
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- Department of Biology, Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
| | - Kriti Agrawal
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- Department of Biology, Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
| | - Maile Ann Young Karris
- Department of Medicine, Division of Infectious Diseases, University of California San Diego, La Jolla, CA, USA
| | - Tariq M. Rana
- Department of Pediatrics, Division of Genetics, Institute for Genomic Medicine, Program in Immunology, University of California San Diego, La Jolla, CA, USA
- UCSD Center for AIDS Research, University of California San Diego, La Jolla, CA, USA
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28
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Song X, Xu C, Wu X, Zhao X, Fan J, Meng S. The potential markers of NK-92 associated to cytotoxicity against K562 cells. Biologicals 2020; 68:46-53. [PMID: 32933840 DOI: 10.1016/j.biologicals.2020.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/21/2020] [Accepted: 08/19/2020] [Indexed: 12/28/2022] Open
Abstract
Markers associated to NK cytolytic activity are in a great need to regulate NK cell immunotherapy products. We assume that biomarkers which response to cytolysis will change their transcription, expression or secretion. To find NK-92 indicator to cytolytic activity, we have evaluated the potential markers by quantifying the expression of well-known cytotoxicity functional molecules (cytokine IFN-γ, Granzyme B, perforin, CD69 and CD107a), and explored candidate markers by a sweeping transcription picture of NK-92 using a direct cytolysis model (incubation with K562). We found that IFN-γ secretion was highly correlated to cytotoxicity of NK-92, neither Granzyme B, perforin secretion, nor CD69, CD107a positive population were upregulated by K562 stimulation. RNAseq revealed 432 genes expression changed during cytolysis, several genes (BIRC3, CSF2, VCAM1 and TNFRSF9) mRNA expression were validated by real time RT-PCR under K562 being killed or protected from being killed conditions. Results suggested IFN-γ secretion, BIRC3 and TNFRSF9 transcription in NK-92 were responsive to K562 cytolysis. In a word, our results confirmed one marker and reveal an array of novel candidate markers associated with NK-92 cytotoxicity. Further studies are greatly needed to determine the roles these new makers play in NK-92 cytolysis process.
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Affiliation(s)
- Xue Song
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China
| | - Chongfeng Xu
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China
| | - Xueling Wu
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China
| | - Xiang Zhao
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China
| | - Jinping Fan
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China
| | - Shufang Meng
- National Cell Collection and Research Center, Institute for Biological Product Control, National Institutes for Food and Drug Control, Tiantan Xili, Dongcheng District, Beijing, 100050, China.
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29
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Murin CD. Considerations of Antibody Geometric Constraints on NK Cell Antibody Dependent Cellular Cytotoxicity. Front Immunol 2020; 11:1635. [PMID: 32849559 PMCID: PMC7406664 DOI: 10.3389/fimmu.2020.01635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
It has been well-established that antibody isotype, glycosylation, and epitope all play roles in the process of antibody dependent cellular cytotoxicity (ADCC). For natural killer (NK) cells, these phenotypes are linked to cellular activation through interaction with the IgG receptor FcγRIIIa, a single pass transmembrane receptor that participates in cytoplasmic signaling complexes. Therefore, it has been hypothesized that there may be underlying spatial and geometric principles that guide proper assembly of an activation complex within the NK cell immune synapse. Further, synergy of antibody phenotypic properties as well as allosteric changes upon antigen binding may also play an as-of-yet unknown role in ADCC. Understanding these facets, however, remains hampered by difficulties associated with studying immune synapse dynamics using classical approaches. In this review, I will discuss relevant NK cell biology related to ADCC, including the structural biology of Fc gamma receptors, and how the dynamics of the NK cell immune synapse are being studied using innovative microscopy techniques. I will provide examples from the literature demonstrating the effects of spatial and geometric constraints on the T cell receptor complex and how this relates to intracellular signaling and the molecular nature of lymphocyte activation complexes, including those of NK cells. Finally, I will examine how the integration of high-throughput and "omics" technologies will influence basic NK cell biology research moving forward. Overall, the goal of this review is to lay a basis for understanding the development of drugs and therapeutic antibodies aimed at augmenting appropriate NK cell ADCC activity in patients being treated for a wide range of illnesses.
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, United States
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30
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Callemeyn J, Lerut E, de Loor H, Arijs I, Thaunat O, Koenig A, Meas-Yedid V, Olivo-Marin JC, Halloran P, Chang J, Thorrez L, Kuypers D, Sprangers B, Van Lommel L, Schuit F, Essig M, Gwinner W, Anglicheau D, Marquet P, Naesens M. Transcriptional Changes in Kidney Allografts with Histology of Antibody-Mediated Rejection without Anti-HLA Donor-Specific Antibodies. J Am Soc Nephrol 2020; 31:2168-2183. [PMID: 32641395 DOI: 10.1681/asn.2020030306] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Circulating donor-specific anti-HLA antibodies (HLA-DSAs) are often absent in serum of kidney allograft recipients whose biopsy specimens demonstrate histology of antibody-mediated rejection (ABMR). It is unclear whether cases involving ABMR histology without detectable HLA-DSAs represent a distinct clinical and molecular phenotype. METHODS In this multicenter cohort study, we integrated allograft microarray analysis with extensive clinical and histologic phenotyping from 224 kidney transplant recipients between 2011 and 2017. We used the term ABMR histology for biopsy specimens that fulfill the first two Banff 2017 criteria for ABMR, irrespective of HLA-DSA status. RESULTS Of 224 biopsy specimens, 56 had ABMR histology; 26 of these (46.4%) lacked detectable serum HLA-DSAs. Biopsy specimens with ABMR histology showed overexpression of transcripts mostly related to IFNγ-induced pathways and activation of natural killer cells and endothelial cells. HLA-DSA-positive and HLA-DSA-negative biopsy specimens with ABMR histology displayed similar upregulation of pathways and enrichment of infiltrating leukocytes. Transcriptional heterogeneity observed in biopsy specimens with ABMR histology was not associated with HLA-DSA status but was caused by concomitant T cell-mediated rejection. Compared with cases lacking ABMR histology, those with ABMR histology and HLA-DSA had higher allograft failure risk (hazard ratio [HR], 7.24; 95% confidence interval [95% CI], 3.04 to 17.20) than cases without HLA-DSA (HR, 2.33; 95% CI, 0.85 to 6.33), despite the absence of transcriptional differences. CONCLUSIONS ABMR histology corresponds to a robust intragraft transcriptional signature, irrespective of HLA-DSA status. Outcome after ABMR histology is not solely determined by the histomolecular presentation but is predicted by the underlying etiologic factor. It is important to consider this heterogeneity in further research and in treatment decisions for patients with ABMR histology.
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Affiliation(s)
- Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Evelyne Lerut
- Department of Morphology and Molecular Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Henriette de Loor
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium.,Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Olivier Thaunat
- Center for Research in Infectious Diseases, Institut National de la Santé et de la Recherche Médicale (INSERM) U1111, Claude Bernard University Lyon I, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University Lyon I, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, France
| | - Alice Koenig
- Center for Research in Infectious Diseases, Institut National de la Santé et de la Recherche Médicale (INSERM) U1111, Claude Bernard University Lyon I, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University Lyon I, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, France
| | - Vannary Meas-Yedid
- Biological Image Analysis Unit, Pasteur Institute, CNRS Unité de Recherche Associée (URA) 2582, Paris, France
| | - Jean-Christophe Olivo-Marin
- Biological Image Analysis Unit, Pasteur Institute, CNRS Unité de Recherche Associée (URA) 2582, Paris, France
| | - Philip Halloran
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jessica Chang
- Division of Nephrology and Transplant Immunology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Lieven Thorrez
- Department of Development and Regeneration, KU Leuven, Kortrijk, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium.,Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Ben Sprangers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Leentje Van Lommel
- Department of Cellular and Molecular Medicine, Gene Expression Unit, KU Leuven, Leuven, Belgium
| | - Frans Schuit
- Department of Cellular and Molecular Medicine, Gene Expression Unit, KU Leuven, Leuven, Belgium
| | - Marie Essig
- Department of Nephrology, Dialysis and Transplantation, University of Limoges, Limoges, France
| | - Wilfried Gwinner
- Department of Nephrology and Internal Medicine, Hannover Medical School, Hannover, Germany
| | - Dany Anglicheau
- Paris Descartes University, Sorbonne Paris Cité University, Paris, France.,INSERM U1151, Paris, France.,Department of Nephrology and Kidney Transplantation, Necker Hospital, Assistance Publique--Hôpitaux de Paris, Paris, France
| | - Pierre Marquet
- INSERM U1248, Limoges, France.,Department of Pharmacology and Toxicology, University Hospitals Limoges, Limoges, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Katholieke Universiteit (KU) Leuven, Leuven, Belgium .,Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
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31
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Aid M, Ram DR, Bosinger SE, Barouch DH, Reeves RK. Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections. Front Cell Infect Microbiol 2020; 10:194. [PMID: 32411625 PMCID: PMC7201019 DOI: 10.3389/fcimb.2020.00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/09/2020] [Indexed: 01/25/2023] Open
Abstract
Natural killer (NK) cells are crucial regulators of antiviral and anti-tumor immune responses. Although in humans some NK cell transcriptional programs are relatively well-established, NK cell transcriptional networks in non-human primates (NHP) remain poorly delineated. Here we performed RNA-Seq experiments using purified NK cells from experimentally naïve rhesus macaques, providing the first transcriptional characterization of pure NK cells in any NHP species. This novel NK cell transcriptomic signature (NK RMtsig) overlaps with published human NK signatures, allowing us to identify new key signaling and transcription factor networks underlying NK cell function. Finally, we show that applying NK RMtsig to an unrelated rhesus macaque cohort infected with SIVmac251 or ZIKV can sensitively detect NK cell repertoire perturbations, thus confirming applicability of this approach. In sum, we propose this NHP NK cell signature will serve as a useful resource for future studies involving infection, disease or treatment modalities in NHP.
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Affiliation(s)
- Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Daniel R Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Steven E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
| | - R Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
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32
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Moar P, Sushmita K, Kateriya S, Tandon R. Transcriptional profiling indicates cAMP-driven reversal of HIV latency in monocytes occurs via transcription factor SP-1. Virology 2020; 542:40-53. [PMID: 32056667 DOI: 10.1016/j.virol.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 01/16/2023]
Abstract
Latent HIV reservoir is a major barrier to absolute HIV cure. Studies on latency reversal agents (LRA) have by far focused mainly on CD4+ T-lymphocytes, while myeloid reservoirs remain under-represented despite their persistence and key contribution to HIV pathogenesis. cAMP has been shown to increase HIV-1 transcription in latently-infected monocytes/macrophages. In this communication, we explored the potential of commercially available pharmacological drugs and phosphodiesterase inhibitors to reactivate HIV in latently-infected monocytic cell-line, U1. We showed that increased levels of intracellular cAMP reverse HIV latency in vitro, which is specific to cells of the myeloid lineage. High throughput RNA-seq analysis revealed that cAMP modulates transcriptional profile of latently HIV-infected cells and provides favourable cellular environment for HIV to produce viral proteins. This reactivation of latent HIV was inhibited by Mithramycin A, a selective Sp1 inhibitor, indicating that the reversal of HIV latency in monocytes is driven by transcription factor Sp1.
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Affiliation(s)
- Preeti Moar
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Kumari Sushmita
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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33
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Liu B, Lindner P, Jirmo AC, Maus U, Illig T, DeLuca DS. A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. BMC Bioinformatics 2020; 21:28. [PMID: 31992182 PMCID: PMC6986093 DOI: 10.1186/s12859-020-3366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step in the analysis process. Gene set enrichment analysis is a standard approach for summarizing differentially expressed genes into pathways or other gene groupings. Here, we explore an alternative approach to utilizing gene sets from curated databases. We examine the method of deriving custom gene sets which may be relevant to a given experiment using reference data sets from previous transcriptomics studies. We call these data-derived gene sets, "gene signatures" for the biological process tested in the previous study. We focus on the feasibility of this approach in analyzing immune-related processes, which are complicated in their nature but play an important role in the medical research. RESULTS We evaluate several statistical approaches to detecting the activity of a gene signature in a target data set. We compare the performance of the data-derived gene signature approach with comparable GO term gene sets across all of the statistical tests. A total of 61 differential expression comparisons generated from 26 transcriptome experiments were included in the analysis. These experiments covered eight immunological processes in eight types of leukocytes. The data-derived signatures were used to detect the presence of immunological processes in the test data with modest accuracy (AUC = 0.67). The performance for GO and literature based gene sets was worse (AUC = 0.59). Both approaches were plagued by poor specificity. CONCLUSIONS When investigators seek to test specific hypotheses, the data-derived signature approach can perform as well, if not better than standard gene-set based approaches for immunological signatures. Furthermore, the data-derived signatures can be generated in the cases that well-defined gene sets are lacking from pathway databases and also offer the opportunity for defining signatures in a cell-type specific manner. However, neither the data-derived signatures nor standard gene-sets can be demonstrated to reliably provide negative predictions for negative cases. We conclude that the data-derived signature approach is a useful and sometimes necessary tool, but analysts should be weary of false positives.
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Affiliation(s)
- Bin Liu
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Adan Chari Jirmo
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Department of Pediatric Pneumology,Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625 Germany
| | - Ulrich Maus
- Division of Experimental Pneumology, Hannover Medical School, Feodor-Lynen-Straße 21, Hannover, 30625 Germany
| | - Thomas Illig
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Straße, Hannover, 30625 Germany
| | - David S. DeLuca
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
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34
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Naluyima P, Lal KG, Costanzo MC, Kijak GH, Gonzalez VD, Blom K, Eller LA, Creegan M, Hong T, Kim D, Quinn TC, Björkström NK, Ljunggren HG, Serwadda D, Katabira ET, Sewankambo NK, Gray RH, Baeten JM, Michael NL, Wabwire-Mangen F, Robb ML, Bolton DL, Sandberg JK, Eller MA. Terminal Effector CD8 T Cells Defined by an IKZF2 +IL-7R - Transcriptional Signature Express FcγRIIIA, Expand in HIV Infection, and Mediate Potent HIV-Specific Antibody-Dependent Cellular Cytotoxicity. THE JOURNAL OF IMMUNOLOGY 2019; 203:2210-2221. [PMID: 31519862 PMCID: PMC6778306 DOI: 10.4049/jimmunol.1900422] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022]
Abstract
Chronic HIV-1 is associated with increased levels of FcγRIIIA+ CD8 T cells. FcγRIIIA+ CD8 T cells display an innate transcriptomic profile akin to NK cells. ADCC is mediated by FcγRIIIA+ CD8 T cells at levels comparable with NK cells.
HIV-1 infection expands large populations of late-stage differentiated CD8 T cells that may persist long after viral escape from TCR recognition. In this study, we investigated whether such CD8 T cell populations can perform unconventional innate-like antiviral effector functions. Chronic untreated HIV-1 infection was associated with elevated numbers of CD45RA+CD57+ terminal effector CD8 T cells expressing FcγRIIIA (CD16). The FcγRIIIA+ CD8 T cells displayed a distinctive transcriptional profile between conventional CD8 T cells and NK cells, characterized by high levels of IKZF2 and low expression of IL7R. This transcriptional profile translated into a distinct NKp80+ IL-7Rα− surface phenotype with high expression of the Helios transcription factor. Interestingly, the FcγRIIIA+ CD8 T cells mediated HIV-specific Ab-dependent cellular cytotoxicity (ADCC) activity at levels comparable with NK cells on a per cell basis. The FcγRIIIA+ CD8 T cells were highly activated in a manner that correlated positively with expansion of the CD8 T cell compartment and with plasma levels of soluble mediators of antiviral immunity and inflammation such as IP-10, TNF, IL-6, and TNFRII. The frequency of FcγRIIIA+ CD8 T cells persisted as patients initiated suppressive antiretroviral therapy, although their activation levels declined. These data indicate that terminally differentiated effector CD8 T cells acquire enhanced innate cell-like characteristics during chronic viral infection and suggest that HIV-specific ADCC is a function CD8 T cells use to target HIV-infected cells. Furthermore, as the FcγRIIIA+ CD8 T cells persist in treatment, they contribute significantly to the ADCC-capable effector cell pool in patients on antiretroviral therapy.
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Affiliation(s)
- Prossy Naluyima
- Makerere University Walter Reed Project, Kampala, Uganda.,Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kerri G Lal
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Margaret C Costanzo
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Veronica D Gonzalez
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Ting Hong
- Department of Global Health, University of Washington School of Public Health, Seattle, WA 98195
| | - Dohoon Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20852.,School of Medicine, Johns Hopkins University, Baltimore, MD 21205
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - David Serwadda
- Rakai Health Sciences Program, Uganda Virus Research Institute, Entebbe, Uganda
| | - Elly T Katabira
- Faculty of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Nelson K Sewankambo
- Faculty of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ronald H Gray
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Jared M Baeten
- Department of Global Health, University of Washington School of Public Health, Seattle, WA 98195.,Department of Medicine, University of Washington School of Public Health, Seattle, WA 98195; and.,Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | | | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Diane L Bolton
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Michael A Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910; .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817
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35
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Zenere G, Olwenyi OA, Byrareddy SN, Braun SE. Optimizing intracellular signaling domains for CAR NK cells in HIV immunotherapy: a comprehensive review. Drug Discov Today 2019; 24:983-991. [PMID: 30771481 PMCID: PMC7065919 DOI: 10.1016/j.drudis.2019.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/16/2019] [Accepted: 02/07/2019] [Indexed: 12/18/2022]
Abstract
Natural killer (NK) cells are innate immune lymphocytes with a key role in host defense against HIV infection. Recent advances in chimeric antigen receptors (CARs) have made NK cells a prime target for expressing recombinant receptors capable of redirecting NK cytotoxic functions towards HIV-infected cells. In this review, we discuss the role of NK cells in HIV and the mechanisms of actions of HIV-targeting CAR strategies. Furthermore, we also review NK cells signal transduction and its application to CAR NK cell strategies to develop new combinations of CAR intracellular domains and to improve CAR NK signaling and cytotoxic functions.
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Affiliation(s)
- Giorgio Zenere
- Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA
| | - Omalla Allan Olwenyi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Siddappa N Byrareddy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA; Department of Cell Biology and Genetics, University of Nebraska Medical Center, Omaha, NE 68198-5880, USA
| | - Stephen E Braun
- Division of Immunology, Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA; Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
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36
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Palgen JL, Tchitchek N, Huot N, Elhmouzi-Younes J, Lefebvre C, Rosenbaum P, Dereuddre-Bosquet N, Martinon F, Hocini H, Cosma A, Müller-Trutwin M, Lévy Y, Le Grand R, Beignon AS. NK cell immune responses differ after prime and boost vaccination. J Leukoc Biol 2019; 105:1055-1073. [PMID: 30794328 DOI: 10.1002/jlb.4a1018-391rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
A better understanding of innate responses induced by vaccination is critical for designing optimal vaccines. Here, we studied the diversity and dynamics of the NK cell compartment after prime-boost immunization with the modified vaccinia virus Ankara using cynomolgus macaques as a model. Mass cytometry was used to deeply characterize blood NK cells. The NK cell subphenotype composition was modified by the prime. Certain phenotypic changes induced by the prime were maintained over time and, as a result, the NK cell composition prior to boost differed from that before prime. The key phenotypic signature that distinguished NK cells responding to the boost from those responding to the prime included stronger expression of several cytotoxic, homing, and adhesion molecules, suggesting that NK cells at recall were functionally distinct. Our data reveal potential priming or imprinting of NK cells after the first vaccine injection. This study provides novel insights into prime-boost vaccination protocols that could be used to optimize future vaccines.
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Affiliation(s)
- Jean-Louis Palgen
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Nicolas Tchitchek
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Nicolas Huot
- Vaccine Research Institute, Henri Mondor Hospital, Créteil, France.,Institut Pasteur, Unit on HIV, Inflammation and Persistence, Paris, France
| | - Jamila Elhmouzi-Younes
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Cécile Lefebvre
- Vaccine Research Institute, Henri Mondor Hospital, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Pierre Rosenbaum
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Nathalie Dereuddre-Bosquet
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Frédéric Martinon
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Hakim Hocini
- Vaccine Research Institute, Henri Mondor Hospital, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Antonio Cosma
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Michaela Müller-Trutwin
- Vaccine Research Institute, Henri Mondor Hospital, Créteil, France.,Institut Pasteur, Unit on HIV, Inflammation and Persistence, Paris, France
| | - Yves Lévy
- Vaccine Research Institute, Henri Mondor Hospital, Créteil, France.,Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Roger Le Grand
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
| | - Anne-Sophie Beignon
- CEA, Université Paris Sud 11, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases, IDMIT, IBFJ, CEA, Fontenay-aux-Roses, France.,Vaccine Research Institute, Henri Mondor Hospital, Créteil, France
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