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Strongin Z, Raymond Marchand L, Deleage C, Pampena MB, Cardenas MA, Beusch CM, Hoang TN, Urban EA, Gourves M, Nguyen K, Tharp GK, Lapp S, Rahmberg AR, Harper J, Del Rio Estrada PM, Gonzalez-Navarro M, Torres-Ruiz F, Luna-Villalobos YA, Avila-Rios S, Reyes-Teran G, Sekaly R, Silvestri G, Kulpa DA, Saez-Cirion A, Brenchley JM, Bosinger SE, Gordon DE, Betts MR, Kissick HT, Paiardini M. Distinct SIV-specific CD8 + T cells in the lymph node exhibit simultaneous effector and stem-like profiles and are associated with limited SIV persistence. Nat Immunol 2024; 25:1245-1256. [PMID: 38886592 DOI: 10.1038/s41590-024-01875-0] [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: 06/16/2023] [Accepted: 05/14/2024] [Indexed: 06/20/2024]
Abstract
Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Laurence Raymond Marchand
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - M Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Christian Michel Beusch
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elizabeth A Urban
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Mael Gourves
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Stacey Lapp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Justin Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Perla M Del Rio Estrada
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Mauricio Gonzalez-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Fernanda Torres-Ruiz
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Yara Andrea Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Santiago Avila-Rios
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Comision Coordinadora de los Institutos Nacionales de Salud y Hospitales de Alta Especialidad, Mexico City, Mexico
| | - Rafick Sekaly
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Asier Saez-Cirion
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris, France
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAIDNIH, Bethesda, MD, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David Ezra Gordon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haydn T Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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2
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Wu J, Li W, Su J, Zheng J, Liang Y, Lin J, Xu B, Liu Y. Integration of single-cell sequencing and bulk RNA-seq to identify and develop a prognostic signature related to colorectal cancer stem cells. Sci Rep 2024; 14:12270. [PMID: 38806611 PMCID: PMC11133358 DOI: 10.1038/s41598-024-62913-3] [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: 01/08/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
The prognosis for patients with colorectal cancer (CRC) remains worse than expected due to metastasis, recurrence, and resistance to chemotherapy. Colorectal cancer stem cells (CRCSCs) play a vital role in tumor metastasis, recurrence, and chemotherapy resistance. However, there are currently no prognostic markers based on CRCSCs-related genes available for clinical use. In this study, single-cell transcriptome sequencing was employed to distinguish cancer stem cells (CSCs) in the CRC microenvironment and analyze their properties at the single-cell level. Subsequently, data from TCGA and GEO databases were utilized to develop a prognostic risk model for CRCSCs-related genes and validate its diagnostic performance. Additionally, functional enrichment, immune response, and chemotherapeutic drug sensitivity of the relevant genes in the risk model were investigated. Lastly, the key gene RPS17 in the risk model was identified as a potential prognostic marker and therapeutic target for further comprehensive studies. Our findings provide new insights into the prognostic treatment of CRC and offer novel perspectives for a systematic and comprehensive understanding of CRC development.
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Affiliation(s)
- Jiale Wu
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Wanyu Li
- Well Lead Medical Co., Ltd., Guangzhou, 511434, Guangdong, China
| | - Junyu Su
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiamin Zheng
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yanwen Liang
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Jiansuo Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Bilian Xu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
| | - Yi Liu
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.
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3
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Kim CG, Kim WK, Kim N, Pyung YJ, Park DJ, Lee JC, Cho CS, Chu H, Yun CH. Intranasal Immunization With Nanoparticles Containing an Orientia tsutsugamushi Protein Vaccine Candidate and a Polysorbitol Transporter Adjuvant Enhances Both Humoral and Cellular Immune Responses. Immune Netw 2023; 23:e47. [PMID: 38188601 PMCID: PMC10767547 DOI: 10.4110/in.2023.23.e47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/09/2024] Open
Abstract
Scrub typhus, a mite-borne infectious disease, is caused by Orientia tsutsugamushi. Despite many attempts to develop a protective strategy, an effective preventive vaccine has not been developed. The identification of appropriate Ags that cover diverse antigenic strains and provide long-lasting immunity is a fundamental challenge in the development of a scrub typhus vaccine. We investigated whether this limitation could be overcome by harnessing the nanoparticle-forming polysorbitol transporter (PST) for an O. tsutsugamushi vaccine strategy. Two target proteins, 56-kDa type-specific Ag (TSA56) and surface cell Ag A (ScaA) were used as vaccine candidates. PST formed stable nano-size complexes with TSA56 (TSA56-PST) and ScaA (ScaA-PST); neither exhibited cytotoxicity. The formation of Ag-specific IgG2a, IgG2b, and IgA in mice was enhanced by intranasal vaccination with TSA56-PST or ScaA-PST. The vaccines containing PST induced Ag-specific proliferation of CD8+ and CD4+ T cells. Furthermore, the vaccines containing PST improved the mouse survival against O. tsutsugamushi infection. Collectively, the present study indicated that PST could enhance both Ag-specific humoral immunity and T cell response, which are essential to effectively confer protective immunity against O. tsutsugamushi infection. These findings suggest that PST has potential for use in an intranasal vaccination strategy.
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Affiliation(s)
- Cheol Gyun Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Korea
| | - Won Kyong Kim
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Health, Cheongju 28159, Korea
| | - Narae Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Young Jin Pyung
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Da-Jeong Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Cheol Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Chong-Su Cho
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyuk Chu
- Division of Zoonotic and Vector Borne Disease Research, Center for Infectious Disease Research, National Institute of Health, Cheongju 28159, Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
- Institutes of Green-bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
- Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul 08826, Korea
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4
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland AM, Short SA, Kheradpour P, Mumbach MR, Franz KM, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors. Clin Immunol 2023; 256:109808. [PMID: 37852344 DOI: 10.1016/j.clim.2023.109808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.
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Affiliation(s)
- Katherine A Drake
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Dimitri Talantov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Benjamin Yuen
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vinod Krishna
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Michelle J Wu
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Sarah A Short
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Pouya Kheradpour
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Maxwell R Mumbach
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Kate M Franz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vladimir Trifonov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Molly V Lucas
- Janssen Research & Development, LLC, NJ, United States of America
| | - James Merson
- Janssen Research & Development, LLC, San Francisco, CA, United States of America
| | - Charles C Kim
- Verily Life Sciences, South San Francisco, CA, United States of America.
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5
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Zhang Y, Bai Y, Ma XX, Song JK, Luo Y, Fei XY, Ru Y, Luo Y, Jiang JS, Zhang Z, Yang D, Xue TT, Zhang HP, Liu TY, Xiang YW, Kuai L, Liu YQ, Li B. Clinical-mediated discovery of pyroptosis in CD8 + T cell and NK cell reveals melanoma heterogeneity by single-cell and bulk sequence. Cell Death Dis 2023; 14:553. [PMID: 37620327 PMCID: PMC10449777 DOI: 10.1038/s41419-023-06068-5] [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: 01/09/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Histologically, melanoma tissues had fewer positive cells percentage of pyroptosis-related genes (PRGs), GZMA, GSDMB, NLRP1, IL18, and CHMP4A in epidermal than in normal skin. Pyroptosis, a new frontier in cancer, affects the tumor microenvironment and tumor immunotherapy. Nevertheless, the role of pyroptosis remains controversial, which reason is partly due to the heterogeneity of the cellular composition in melanoma. In this study, we present a comprehensive analysis of the single-cell transcriptome landscape of pyroptosis in melanoma specimens. Our findings reveal dysregulation in the expression of PRGs, particularly in immune cells, such as CD8+ cells (representing CD8+ T cells) and CD57+ cells (representing NK cells). Additionally, the immunohistochemical and multiplex immunofluorescence staining experiments results further confirmed GZMA+ cells and GSDMB+ cells were predominantly expressed in immune cells, especially in CD8 + T cells and NK cells. Melanoma specimens secreted a minimal presence of GZMA+ merged CD8+ T cells (0.11%) and GSDMB+ merged CD57+ cells (0.08%), compared to the control groups exhibiting proportions of 4.02% and 0.62%, respectively. The aforementioned findings indicate that a reduced presence of immune cells within tumors may play a role in diminishing the ability of pyroptosis, consequently posing a potential risk to the anti-melanoma properties. To quantify clinical relevance, we constructed a prognostic risk model and an individualized nomogram (C-index=0.58, P = 0.002), suggesting a potential role of PRGs in malignant melanoma prevention. In conclusion, our integrated single-cell and bulk RNA-seq analysis identified immune cell clusters and immune gene modules with experiment validation, contributing to our better understanding of pyroptosis in melanoma.
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Grants
- This study was supported by Shanghai Clinical Key Specialty Construction Project (shslczdzk05001), Shanghai Science and Technology Committee (21Y21920101,21Y21920102), the Shanghai Development Office of TCM (ZY(2021-2023)-0302, ZY(2021-2023)-0209-13).
- the Key Project of Clinical Research from Shanghai Hospital Development Center (SHDC2020CR4020), and Funding from Shanghai Skin Disease Hospital (2018KYQD01).
- Shanghai Municipal Commission of Economy and Information Technology, Shanghai Artificial Intelligence Innovation and Development Project-Intelligent Dermatology Clinic Based on Modern TCM Diagnostic Technology, No. 2020-RGZN-02038.
- the Youth Talent Promotion Project of China Association of Traditional Chinese Medicine (2021-2023) Category A (CACM-2021-QNRC2-A10), the “Chen Guang” project supported by Shanghai Municipal Education Commission and Shanghai Education Development Foundation (22CGA50), the Health Young Talents of Shanghai Municipal Health Commission (2022YQ026), the Xinglin Youth Scholar of Shanghai University of Traditional Chinese Medicine (No. RY411.33.10).
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Affiliation(s)
- Ying Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yun Bai
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Xiao-Xuan Ma
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jian-Kun Song
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Yue Luo
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Xiao-Ya Fei
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jing-Si Jiang
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Zhan Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dan Yang
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China
| | - Ting-Ting Xue
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hui-Ping Zhang
- Shanghai Applied Protein Technology Co., Ltd., 58 Yuanmei Road, Shanghai, 200233, China
| | - Tai-Yi Liu
- Shanghai Applied Protein Technology Co., Ltd., 58 Yuanmei Road, Shanghai, 200233, China
| | - Yan-Wei Xiang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Ye-Qiang Liu
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
| | - Bin Li
- Shanghai Skin Disease Hospital, Tongji University, Shanghai, 200443, China.
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 201203, China.
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6
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland A, Short SA, Kheradpour P, Mumbach M, Franz K, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542297. [PMID: 37292797 PMCID: PMC10246026 DOI: 10.1101/2023.05.25.542297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. Additionally, in the lymphocyte compartment, CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19.
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Affiliation(s)
| | | | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA
| | | | | | | | | | | | | | | | | | - Kate Franz
- Verily Life Sciences, South San Francisco, CA
| | | | | | - James Merson
- Janssen Research & Development, LLC, San Diego, CA
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7
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La Manna MP, Shekarkar Azgomi M, Tamburini B, Badami GD, Mohammadnezhad L, Dieli F, Caccamo N. Phenotypic and Immunometabolic Aspects on Stem Cell Memory and Resident Memory CD8+ T Cells. Front Immunol 2022; 13:884148. [PMID: 35784300 PMCID: PMC9247337 DOI: 10.3389/fimmu.2022.884148] [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: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The immune system, smartly and surprisingly, saves the exposure of a particular pathogen in its memory and reacts to the pathogen very rapidly, preventing serious diseases.Immunologists have long been fascinated by understanding the ability to recall and respond faster and more vigorously to a pathogen, known as “memory”.T-cell populations can be better described by using more sophisticated techniques to define phenotype, transcriptional and epigenetic signatures and metabolic pathways (single-cell resolution), which uncovered the heterogeneity of the memory T-compartment. Phenotype, effector functions, maintenance, and metabolic pathways help identify these different subsets. Here, we examine recent developments in the characterization of the heterogeneity of the memory T cell compartment. In particular, we focus on the emerging role of CD8+ TRM and TSCM cells, providing evidence on how their immunometabolism or modulation can play a vital role in their generation and maintenance in chronic conditions such as infections or autoimmune diseases.
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Affiliation(s)
- Marco Pio La Manna
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Mojtaba Shekarkar Azgomi
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Bartolo Tamburini
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Giusto Davide Badami
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Leila Mohammadnezhad
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Francesco Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Nadia Caccamo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
- *Correspondence: Nadia Caccamo,
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8
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Kok L, Masopust D, Schumacher TN. The precursors of CD8 + tissue resident memory T cells: from lymphoid organs to infected tissues. Nat Rev Immunol 2022; 22:283-293. [PMID: 34480118 PMCID: PMC8415193 DOI: 10.1038/s41577-021-00590-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
CD8+ tissue resident memory T cells (TRM cells) are essential for immune defence against pathogens and malignancies, and the molecular processes that lead to TRM cell formation are therefore of substantial biomedical interest. Prior work has demonstrated that signals present in the inflamed tissue micro-environment can promote the differentiation of memory precursor cells into mature TRM cells, and it was therefore long assumed that TRM cell formation adheres to a 'local divergence' model, in which TRM cell lineage decisions are exclusively made within the tissue. However, a growing body of work provides evidence for a 'systemic divergence' model, in which circulating T cells already become preconditioned to preferentially give rise to the TRM cell lineage, resulting in the generation of a pool of TRM cell-poised T cells within the lymphoid compartment. Here, we review the emerging evidence that supports the existence of such a population of circulating TRM cell progenitors, discuss current insights into their formation and highlight open questions in the field.
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Affiliation(s)
- Lianne Kok
- grid.430814.a0000 0001 0674 1393Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - David Masopust
- grid.17635.360000000419368657Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN USA
| | - Ton N. Schumacher
- grid.430814.a0000 0001 0674 1393Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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9
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Smith RL, Goddard A, Boddapati A, Brooks S, Schoeman JP, Lack J, Leisewitz A, Ackerman H. Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host. BMC Genomics 2021; 22:619. [PMID: 34399690 PMCID: PMC8369750 DOI: 10.1186/s12864-021-07889-4] [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: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 12/02/2022] Open
Abstract
Background Babesia rossi is a leading cause of morbidity and mortality among the canine population of sub-Saharan Africa, but pathogenesis remains poorly understood. Previous studies of B. rossi infection were derived from clinical cases, in which neither the onset of infection nor the infectious inoculum was known. Here, we performed controlled B. rossi inoculations in canines and evaluated disease progression through clinical tests and whole blood transcriptomic profiling. Results Two subjects were administered a low inoculum (104 parasites) while three received a high (108 parasites). Subjects were monitored for 8 consecutive days; anti-parasite treatment with diminazene aceturate was administered on day 4. Blood was drawn prior to inoculation as well as every experimental day for assessment of clinical parameters and transcriptomic profiles. The model recapitulated natural disease manifestations including anemia, acidosis, inflammation and behavioral changes. Rate of disease onset and clinical severity were proportional to the inoculum. To analyze the temporal dynamics of the transcriptomic host response, we sequenced mRNA extracted from whole blood drawn on days 0, 1, 3, 4, 6, and 8. Differential gene expression, hierarchical clustering, and pathway enrichment analyses identified genes and pathways involved in response to hemolysis, metabolic changes, and several arms of the immune response including innate immunity, adaptive immunity, and response to viral infection. Conclusions This work comprehensively characterizes the clinical and transcriptomic progression of B. rossi infection in canines, thus establishing a large mammalian model of severe hemoprotozoal disease to facilitate the study of host-parasite biology and in which to test novel anti-disease therapeutics. The knowledge gained from the study of B. rossi in canines will not only improve our understanding of this emerging infectious disease threat in domestic dogs, but also provide insight into the pathobiology of human diseases caused by Babesia and Plasmodium species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07889-4.
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Affiliation(s)
- Rachel L Smith
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD, 20852, USA
| | - Amelia Goddard
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria, 0110, South Africa
| | - Arun Boddapati
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20894, USA.,Advanced Biomedical Computational Science (ABCS), Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Steven Brooks
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD, 20852, USA
| | - Johan P Schoeman
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria, 0110, South Africa
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20894, USA.,Advanced Biomedical Computational Science (ABCS), Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Andrew Leisewitz
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, Pretoria, 0110, South Africa.
| | - Hans Ackerman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, MD, 20852, USA.
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10
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Wang D, Prager BC, Gimple RC, Aguilar B, Alizadeh D, Tang H, Lv D, Starr R, Brito A, Wu Q, Kim LJY, Qiu Z, Lin P, Lorenzini MH, Badie B, Forman SJ, Xie Q, Brown CE, Rich JN. CRISPR Screening of CAR T Cells and Cancer Stem Cells Reveals Critical Dependencies for Cell-Based Therapies. Cancer Discov 2020; 11:1192-1211. [PMID: 33328215 DOI: 10.1158/2159-8290.cd-20-1243] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/02/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Glioblastoma (GBM) contains self-renewing GBM stem cells (GSC) potentially amenable to immunologic targeting, but chimeric antigen receptor (CAR) T-cell therapy has demonstrated limited clinical responses in GBM. Here, we interrogated molecular determinants of CAR-mediated GBM killing through whole-genome CRISPR screens in both CAR T cells and patient-derived GSCs. Screening of CAR T cells identified dependencies for effector functions, including TLE4 and IKZF2. Targeted knockout of these genes enhanced CAR antitumor efficacy. Bulk and single-cell RNA sequencing of edited CAR T cells revealed transcriptional profiles of superior effector function and inhibited exhaustion responses. Reciprocal screening of GSCs identified genes essential for susceptibility to CAR-mediated killing, including RELA and NPLOC4, the knockout of which altered tumor-immune signaling and increased responsiveness of CAR therapy. Overall, CRISPR screening of CAR T cells and GSCs discovered avenues for enhancing CAR therapeutic efficacy against GBM, with the potential to be extended to other solid tumors. SIGNIFICANCE: Reciprocal CRISPR screening identified genes in both CAR T cells and tumor cells regulating the potency of CAR T-cell cytotoxicity, informing molecular targeting strategies to potentiate CAR T-cell antitumor efficacy and elucidate genetic modifications of tumor cells in combination with CAR T cells to advance immuno-oncotherapy.This article is highlighted in the In This Issue feature, p. 995.
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Affiliation(s)
- Dongrui Wang
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Briana C Prager
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Cleveland Clinic Lerner College of Medicine at Cleveland Clinic and Case Western Reserve University, Cleveland, Ohio.,Sanford Consortium for Regenerative Medicine, La Jolla, California
| | - Ryan C Gimple
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Brenda Aguilar
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Darya Alizadeh
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Hongzhen Tang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Deguan Lv
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California
| | - Renate Starr
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Alfonso Brito
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Qiulian Wu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California
| | - Leo J Y Kim
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Zhixin Qiu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California
| | - Peng Lin
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Michael H Lorenzini
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California.,Sanford Consortium for Regenerative Medicine, La Jolla, California
| | - Behnam Badie
- Division of Neurosurgery, Department of Surgery, City of Hope, Duarte, California
| | - Stephen J Forman
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California
| | - Qi Xie
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Christine E Brown
- T Cell Therapeutics Research Labs, Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, California.
| | - Jeremy N Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, California. .,Sanford Consortium for Regenerative Medicine, La Jolla, California.,University of Pittsburgh Medical Center Hillman Cancer Center, Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
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11
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Meziane O, Alexandrova Y, Olivenstein R, Dupuy FP, Salahuddin S, Thomson E, Orlova M, Schurr E, Ancuta P, Durand M, Chomont N, Estaquier J, Bernard NF, Costiniuk CT, Jenabian MA. Peculiar Phenotypic and Cytotoxic Features of Pulmonary Mucosal CD8 T Cells in People Living with HIV Receiving Long-Term Antiretroviral Therapy. THE JOURNAL OF IMMUNOLOGY 2020; 206:641-651. [PMID: 33318292 DOI: 10.4049/jimmunol.2000916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 12/31/2022]
Abstract
People living with HIV have high burdens of chronic lung disease, lung cancers, and pulmonary infections despite antiretroviral therapy (ART). The rates of tobacco smoking by people living with HIV vastly exceed that of the general population. Furthermore, we showed that HIV can persist within the lung mucosa despite long-term ART. As CD8 T cell cytotoxicity is pivotal for controlling viral infections and eliminating defective cells, we explored the phenotypic and functional features of pulmonary versus peripheral blood CD8 T cells in ART-treated HIV+ and uninfected controls. Bronchoalveolar lavage fluid and matched blood were obtained from asymptomatic ART-treated HIV+ smokers (n = 11) and nonsmokers (n = 15) and uninfected smokers (n = 7) and nonsmokers (n = 10). CD8 T cell subsets and phenotypes were assessed by flow cytometry. Perforin/granzyme B content, degranulation (CD107a expression), and cytotoxicity against autologous Gag peptide-pulsed CD4 T cells (Annexin V+) following in vitro stimulation were assessed. In all groups, pulmonary CD8 T cells were enriched in effector memory subsets compared with blood and displayed higher levels of activation (HLA-DR+) and exhaustion (PD1+) markers. Significant reductions in proportions of senescent pulmonary CD28-CD57+ CD8 T cells were observed only in HIV+ smokers. Pulmonary CD8 T cells showed lower perforin expression ex vivo compared with blood CD8 T cells, with reduced granzyme B expression only in HIV+ nonsmokers. Bronchoalveolar lavage CD8 T cells showed significantly less in vitro degranulation and CD4 killing capacity than blood CD8 T cells. Therefore, pulmonary mucosal CD8 T cells are more differentiated, activated, and exhausted, with reduced killing capacity in vitro than blood CD8 T cells, potentially contributing to a suboptimal anti-HIV immune response within the lungs.
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Affiliation(s)
- Oussama Meziane
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec H2X 1Y4, Canada
| | - Yulia Alexandrova
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec H2X 1Y4, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Ronald Olivenstein
- Division of Respirology, Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Franck P Dupuy
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Syim Salahuddin
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec H2X 1Y4, Canada
| | - Elaine Thomson
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec H2X 1Y4, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Marianna Orlova
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Petronela Ancuta
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada.,Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Madeleine Durand
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec H2X 0A9, Canada.,Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Jérôme Estaquier
- Centre de Recherche du Centre Hospitalier Universitaire de Québec, Faculté de Médecine, Université Laval, Quebec City, Quebec G1V 4G2, Canada
| | - Nicole F Bernard
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Division of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada.,Division of Clinical Immunology, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada; and
| | - Cecilia T Costiniuk
- Infectious Diseases and Immunity in Global Health Program, Research Institute of McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.,Chronic Viral Illness Service, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,Division of Infectious Diseases, McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada
| | - Mohammad-Ali Jenabian
- Département des Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec H2X 1Y4, Canada; .,Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada.,Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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12
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HIV Infection and Persistence in Pulmonary Mucosal Double Negative T Cells In Vivo. J Virol 2020; 94:JVI.01788-20. [PMID: 32967958 PMCID: PMC7925170 DOI: 10.1128/jvi.01788-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 11/20/2022] Open
Abstract
The lungs are relatively unexplored anatomical human immunodeficiency virus (HIV) reservoirs in the antiretroviral therapy (ART) era. Double negative (DN) T cells are a subset of T cells that lack expression of CD4 and CD8 (CD4- CD8-) and may have both regulatory and effector functions during HIV infection. Notably, circulating DN T cells were previously described as cellular HIV reservoirs. Here, we undertook a thorough analysis of pulmonary versus blood DN T cells of people living with HIV (PLWH) under ART. Bronchoalveolar lavage (BAL) fluid and matched peripheral blood were collected from 35 PLWH on ART and 16 uninfected volunteers without respiratory symptoms. Both PLWH and HIV-negative (HIV-) adults displayed higher frequencies of DN T cells in BAL versus blood, and these cells mostly exhibited an effector memory phenotype. In PLWH, pulmonary mucosal DN T cells expressed higher levels of HLA-DR and several cellular markers associated with HIV persistence (CCR6, CXCR3, and PD-1) than blood. We also observed that DN T cells were less senescent (CD28- CD57+) and expressed less immunosuppressive ectonucleotidase (CD73/CD39), granzyme B, and perforin in the BAL fluid than in the blood of PLWH. Importantly, fluorescence-activated cell sorter (FACS)-sorted DN T cells from the BAL fluid of PLWH under suppressive ART harbored HIV DNA. Using the humanized bone marrow-liver-thymus (hu-BLT) mouse model of HIV infection, we observed higher infection frequencies of lung DN T cells than those of the blood and spleen in both early and late HIV infection. Overall, our findings show that HIV is seeded in pulmonary mucosal DN T cells early following infection and persists in these potential cellular HIV reservoirs even during long-term ART.IMPORTANCE Reservoirs of HIV during ART are the primary reasons why HIV/AIDS remains an incurable disease. Indeed, HIV remains latent and unreachable by antiretrovirals in cellular and anatomical sanctuaries, preventing its eradication. The lungs have received very little attention compared to other anatomical reservoirs despite being immunological effector sites exhibiting characteristics ideal for HIV persistence. Furthermore, PLWH suffer from a high burden of pulmonary non-opportunistic infections, suggesting impaired pulmonary immunity despite ART. Meanwhile, various immune cell populations have been proposed to be cellular reservoirs in blood, including CD4- CD8- DN T cells, a subset that may originate from CD4 downregulation by HIV proteins. The present study aims to describe DN T cells in human and humanized mice lungs in relation to intrapulmonary HIV burden. The characterization of DN T cells as cellular HIV reservoirs and the lungs as an anatomical HIV reservoir will contribute to the development of targeted HIV eradication strategies.
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13
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Nguyen S, Sada-Japp A, Petrovas C, Betts MR. Jigsaw falling into place: A review and perspective of lymphoid tissue CD8+ T cells and control of HIV. Mol Immunol 2020; 124:42-50. [PMID: 32526556 PMCID: PMC7279761 DOI: 10.1016/j.molimm.2020.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
CD8+ T cells are crucial for immunity against viral infections, including HIV. Several characteristics of CD8+ T cells, such as polyfunctionality and cytotoxicity, have been correlated with effective control of HIV. However, most of these correlates have been established in the peripheral blood. Meanwhile, HIV primarily replicates in lymphoid tissues. Therefore, it is unclear which aspects of CD8+ T cell biology are shared and which are different between blood and lymphoid tissues in the context of HIV infection. In this review, we will recapitulate the latest advancements of our knowledge on lymphoid tissue CD8+ T cells during HIV infection and discuss the insights these advancements might provide for the development of a HIV cure.
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Affiliation(s)
- Son Nguyen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alberto Sada-Japp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Constantinos Petrovas
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Rodriguez-Garcia M, Shen Z, Fortier JM, Wira CR. Differential Cytotoxic Function of Resident and Non-resident CD8+ T Cells in the Human Female Reproductive Tract Before and After Menopause. Front Immunol 2020; 11:1096. [PMID: 32582183 PMCID: PMC7287154 DOI: 10.3389/fimmu.2020.01096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/06/2020] [Indexed: 01/22/2023] Open
Abstract
The functional characterization and regulation of tissue resident and non-resident CD8+ T cells in the human female reproductive tract (FRT) as women age remains a gap in our knowledge. Here we characterized the cytotoxic activity and granular contents of CD8+ T cells from the FRT in pre- and postmenopausal women. We found that under steady-state conditions, CD8+ T cells from endometrium (EM), endocervix and ectocervix displayed direct cytotoxic activity, and that cytotoxicity increased in the EM after menopause. Cytotoxic activity was sensitive to suppression by TGFβ exclusively in the EM, and sensitivity to TGFβ was reduced after menopause. Under steady-state conditions, cytotoxic activity (measured as direct killing activity), cytotoxic potential (measured as content of cytotoxic molecules) and proliferation are enhanced in non-resident CD8+ (CD103−) T cells compared to tissue resident (CD103+) T cells. Upon activation, CD103+ T cells displayed greater degranulation compared to CD103− T cells, however the granular content of perforin, granzyme A (GZA) or granzyme B (GZB) was significantly lower. After menopause, degranulation significantly increased, and granular release switched from predominantly GZB in premenopausal to GZA in postmenopausal women. Postmenopausal changes affected both CD103+ and CD103− subpopulations. Finally, CD103+ T cells displayed reduced proliferation compared to CD103− T cells, but after proliferation, cytotoxic molecules were similar in each population. Our results highlight the complexity of regulation of cytotoxic function in the FRT before and after menopause, and are relevant to the development of protective strategies against genital infections and gynecological cancers as women age.
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Affiliation(s)
- Marta Rodriguez-Garcia
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States.,Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
| | - Zheng Shen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Jared M Fortier
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Charles R Wira
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
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15
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Abstract
PURPOSE OF REVIEW This review summarizes our current understanding of HIV-1-specific T-cell responses in mucosal tissues, emphasizing recent work and specifically highlighting papers published over the past 18 months. RECENT FINDINGS Recent work has improved the standardization of tissue sampling approaches and provided new insights on the abundance, phenotype and distribution of HIV-1-specific T-cell populations in mucosal tissues. In addition, it has recently been established that some lymphocytes exist in tissues as "permanent resident" memory cells that differ from their counterparts in blood. SUMMARY HIV-1-specific T-cell responses have been extensively characterized; however, the vast majority of reports have focused on T-cells isolated from peripheral blood. Mucosal tissues of the genitourinary and gastrointestinal tracts serve as the primary sites of HIV-1 transmission, and provide "front line" barrier defenses against HIV-1 and other pathogens. In addition, the gastrointestinal tract remains a significant viral reservoir throughout the chronic phase of infection. Tissue-based immune responses may be critical in fighting infection, and understanding these defenses may lead to improved vaccines and immunotherapeutic strategies.
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16
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Schanoski AS, Le TT, Kaiserman D, Rowe C, Prow NA, Barboza DD, Santos CA, Zanotto PMA, Magalhães KG, Aurelio L, Muller D, Young P, Zhao P, Bird PI, Suhrbier A. Granzyme A in Chikungunya and Other Arboviral Infections. Front Immunol 2020; 10:3083. [PMID: 31993061 PMCID: PMC6971054 DOI: 10.3389/fimmu.2019.03083] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/17/2019] [Indexed: 12/23/2022] Open
Abstract
Granzyme A (GzmA) is secreted by cytotoxic lymphocytes and has traditionally been viewed as a mediator of cell death. However, a growing body of data suggests the physiological role of GzmA is promotion of inflammation. Here, we show that GzmA is significantly elevated in the sera of chikungunya virus (CHIKV) patients and that GzmA levels correlated with viral loads and disease scores in these patients. Serum GzmA levels were also elevated in CHIKV mouse models, with NK cells the likely source. Infection of mice deficient in type I interferon responses with CHIKV, Zika virus, or dengue virus resulted in high levels of circulating GzmA. We also show that subcutaneous injection of enzymically active recombinant mouse GzmA was able to mediate inflammation, both locally at the injection site as well as at a distant site. Protease activated receptors (PARs) may represent targets for GzmA, and we show that treatment with PAR antagonist ameliorated GzmA- and CHIKV-mediated inflammation.
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Affiliation(s)
| | - Thuy T Le
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Dion Kaiserman
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Caitlin Rowe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Natalie A Prow
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Diego D Barboza
- Bacteriology Laboratory, Butantan Institute, São Paulo, Brazil
| | - Cliomar A Santos
- Health Foundation Parreiras Horta, Central Laboratory of Public Health, State Secretary for Health, Aracajú, Brazil
| | - Paolo M A Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly G Magalhães
- Laboratory of Immunology and Inflammation, University of Brasilia, Brasilia, Brazil
| | - Luigi Aurelio
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - David Muller
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Paul Young
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Peishen Zhao
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Phillip I Bird
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Disease Research Centre, University of Queensland, Brisbane, QLD, Australia
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17
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Kim GB, Hege K, Riley JL. CAR Talk: How Cancer-Specific CAR T Cells Can Instruct How to Build CAR T Cells to Cure HIV. Front Immunol 2019; 10:2310. [PMID: 31611880 PMCID: PMC6776630 DOI: 10.3389/fimmu.2019.02310] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/12/2019] [Indexed: 01/21/2023] Open
Abstract
Re-directing T cells via chimeric antigen receptors (CARs) was first tested in HIV-infected individuals with limited success, but these pioneering studies laid the groundwork for the clinically successful CD19 CARs that were recently FDA approved. Now there is great interest in revisiting the concept of using CAR-expressing T cells as part of a strategy to cure HIV. Many lessons have been learned on how to best engineer T cells to cure cancer, but not all of these lessons apply when developing CARs to treat and cure HIV. This mini review will focus on how early CAR T cell studies in HIV paved the way for cancer CAR T cell therapy and how progress in cancer CAR therapy has and will continue to be instructive for the development of HIV CAR T cell therapy. Additionally, the unique challenges that must be overcome to develop a successful HIV CAR T cell therapy will be highlighted.
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Affiliation(s)
- Gloria B. Kim
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kristen Hege
- Celgene Corporation, San Francisco, CA, United States
| | - James L. Riley
- Department of Microbiology, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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18
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Perdomo-Celis F, Taborda NA, Rugeles MT. CD8 + T-Cell Response to HIV Infection in the Era of Antiretroviral Therapy. Front Immunol 2019; 10:1896. [PMID: 31447862 PMCID: PMC6697065 DOI: 10.3389/fimmu.2019.01896] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Although the combined antiretroviral therapy (cART) has decreased the deaths associated with the immune deficiency acquired syndrome (AIDS), non-AIDS conditions have emerged as an important cause of morbidity and mortality in HIV-infected patients under suppressive cART. Since these conditions are associated with a persistent inflammatory and immune activation state, major efforts are currently made to improve the immune reconstitution. CD8+ T-cells are critical in the natural and cART-induced control of viral replication; however, CD8+ T-cells are highly affected by the persistent immune activation and exhaustion state driven by the increased antigenic and inflammatory burden during HIV infection, inducing phenotypic and functional alterations, and hampering their antiviral response. Several CD8+ T-cell subsets, such as interleukin-17-producing and follicular CXCR5+ CD8+ T-cells, could play a particular role during HIV infection by promoting the gut barrier integrity, and exerting viral control in lymphoid follicles, respectively. Here, we discuss the role of CD8+ T-cells and some of their subpopulations during HIV infection in the context of cART-induced viral suppression, focusing on current challenges and alternatives for reaching complete reconstitution of CD8+ T-cells antiviral function. We also address the potential usefulness of CD8+ T-cell features to identify patients who will reach immune reconstitution or have a higher risk for developing non-AIDS conditions. Finally, we examine the therapeutic potential of CD8+ T-cells for HIV cure strategies.
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Affiliation(s)
- Federico Perdomo-Celis
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia
| | - Natalia A Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia.,Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia
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19
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Huff WX, Kwon JH, Henriquez M, Fetcko K, Dey M. The Evolving Role of CD8 +CD28 - Immunosenescent T Cells in Cancer Immunology. Int J Mol Sci 2019; 20:ijms20112810. [PMID: 31181772 PMCID: PMC6600236 DOI: 10.3390/ijms20112810] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022] Open
Abstract
Functional, tumor-specific CD8+ cytotoxic T lymphocytes drive the adaptive immune response to cancer. Thus, induction of their activity is the ultimate aim of all immunotherapies. Success of anti-tumor immunotherapy is precluded by marked immunosuppression in the tumor microenvironment (TME) leading to CD8+ effector T cell dysfunction. Among the many facets of CD8+ T cell dysfunction that have been recognized—tolerance, anergy, exhaustion, and senescence—CD8+ T cell senescence is incompletely understood. Naïve CD8+ T cells require three essential signals for activation, differentiation, and survival through T-cell receptor, costimulatory receptors, and cytokine receptors. Downregulation of costimulatory molecule CD28 is a hallmark of senescent T cells and increased CD8+CD28− senescent populations with heterogeneous roles have been observed in multiple solid and hematogenous tumors. T cell senescence can be induced by several factors including aging, telomere damage, tumor-associated stress, and regulatory T (Treg) cells. Tumor-induced T cell senescence is yet another mechanism that enables tumor cell resistance to immunotherapy. In this paper, we provide a comprehensive overview of CD8+CD28− senescent T cell population, their origin, their function in immunology and pathologic conditions, including TME and their implication for immunotherapy. Further characterization and investigation into this subset of CD8+ T cells could improve the efficacy of future anti-tumor immunotherapy.
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Affiliation(s)
- Wei X Huff
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Jae Hyun Kwon
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Mario Henriquez
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Kaleigh Fetcko
- Department of Neurology, University of Illinois at Chicago School of Medicine, Chicago, IL 60612, USA.
| | - Mahua Dey
- Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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20
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Zhao Y, Li X, Zhao W, Wang J, Yu J, Wan Z, Gao K, Yi G, Wang X, Fan B, Wu Q, Chen B, Xie F, Wu J, Zhang W, Chen F, Yang H, Wang J, Xu X, Li B, Liu S, Hou Y, Liu X. Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood. Gigascience 2019; 8:giz047. [PMID: 31049560 PMCID: PMC6497034 DOI: 10.1093/gigascience/giz047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/30/2019] [Accepted: 04/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND For both pediatric and adult patients, umbilical cord blood (UCB) transplant is a therapeutic option for a variety of hematologic diseases, such as blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in UCB has not yet been assessed in an unbiased and systemic fashion. In the present study, nucleated cells from UCB were subjected to single-cell RNA sequencing to simultaneously profile the gene expression signatures of thousands of cells, generating a rich resource for further functional studies. Here, we report the transcriptomes of 17,637 UCB cells, covering 12 major cell types, many of which can be further divided into distinct subpopulations. RESULTS Pseudotemporal ordering of nucleated red blood cells identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect nucleated red blood cell maturation. Progenitor cells in UCB also comprise 2 subpopulations with activation of divergent transcription programs, leading to specific cell fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in natural killer and natural killer T-cell types in UCB. CONCLUSIONS Taken together, our data form a comprehensive single-cell transcriptomic landscape that reveals previously unrecognized cell types, pathways, and mechanisms of gene expression regulation. These data may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.
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Affiliation(s)
- Yi Zhao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Weihua Zhao
- Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, China
| | | | - Jiawei Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ziyun Wan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kai Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Gang Yi
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Bingbing Fan
- Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, Guangdong Province, China
| | - Qinkai Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Feng Xie
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | | | - Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Bin Li
- BGI-Shenzhen, Shenzhen 518083, China
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
- Department of Immunology and Microbiology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | | | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen 518083, China
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21
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Warren JA, Clutton G, Goonetilleke N. Harnessing CD8 + T Cells Under HIV Antiretroviral Therapy. Front Immunol 2019; 10:291. [PMID: 30863403 PMCID: PMC6400228 DOI: 10.3389/fimmu.2019.00291] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Antiretroviral therapy (ART) has transformed HIV from a fatal disease to a chronic condition. In recent years there has been considerable interest in strategies to enable HIV-infected individuals to cease ART without viral rebound, either by purging all cells infected harboring replication-competent virus (HIV eradication), or by boosting immune responses to allow durable suppression of virus without rebound (HIV remission). Both of these approaches may need to harness HIV-specific CD8+ T cells to eliminate infected cells and/or prevent viral spread. In untreated infection, both HIV-specific and total CD8+ T cells are dysfunctional. Here, we review our current understanding of both global and HIV-specific CD8+ T cell immunity in HIV-infected individuals with durably suppressed viral load under ART, and its implications for HIV cure, eradication or remission. Overall, the literature indicates significant normalization of global T cell parameters, including CD4/8 ratio, activation status, and telomere length. Global characteristics of CD8+ T cells from HIV+ART+ individuals align more closely with those of HIV-seronegative individuals than of viremic HIV-infected individuals. However, markers of senescence remain elevated, leading to the hypothesis that immune aging is accelerated in HIV-infected individuals on ART. This phenomenon could have implications for attempts to prime de novo, or boost existing HIV-specific CD8+ T cell responses. A major challenge for both HIV cure and remission strategies is to elicit HIV-specific CD8+ T cell responses superior to that elicited by natural infection in terms of response kinetics, magnitude, breadth, viral suppressive capacity, and tissue localization. Addressing these issues will be critical to the success of HIV cure and remission attempts.
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Affiliation(s)
- Joanna A Warren
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC, United States
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22
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Perdomo-Celis F, Velilla PA, Taborda NA, Rugeles MT. An altered cytotoxic program of CD8+ T-cells in HIV-infected patients despite HAART-induced viral suppression. PLoS One 2019; 14:e0210540. [PMID: 30625227 PMCID: PMC6326488 DOI: 10.1371/journal.pone.0210540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/27/2018] [Indexed: 01/30/2023] Open
Abstract
Despite the suppression of viral replication induced by the highly active anti-retroviral therapy (HAART), an increased immune activation and inflammatory state persists in HIV-infected patients, contributing to lower treatment response and immune reconstitution, and development of non-AIDS conditions. The chronic activation and inflammation affect the functionality and differentiation of CD8+ T-cells, particularly reducing their cytotoxic capacity, which is critical in the control of HIV replication. Although previous studies have shown that HAART induce a partial immune reconstitution, its effect on CD8+ T-cells cytotoxic function, as well as its relationship with the inflammatory state, is yet to be defined. Here, we characterized the functional profile of polyclonal and HIV-specific CD8+ T cells, based on the expression of cell activation and differentiation markers, in individuals chronically infected with HIV, under HAART. Compared with seronegative controls, CD8+ T-cells from patients on HAART exhibited a low degranulation capacity (surface expression of CD107a), with consequent low secreted levels and high intracellular expression of granzyme B and perforin. This degranulation defect was particularly observed in those cells expressing the activation marker HLA-DR, which were further characterized as effector memory cells with high expression of CD57. The expression of CD107a, but not of granzyme B and perforin, in CD8+ T-cells from HIV-infected patients on HAART reached levels similar to those in seronegative controls when the treatment duration was higher than 25 months. In addition, the expression of CD107a was negatively correlated with the expression of exhaustion markers on CD8+ T-cells and the plasma inflammatory molecule sCD14. Thus, despite HAART-induced viral suppression, CD8+ T-cells from HIV-infected patients have an alteration in their cytotoxic program. This defect is associated with the cellular activation, differentiation and exhaustion state, as well as with the inflammation levels, and can be partially recovered with a long and continuous treatment.
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Affiliation(s)
- Federico Perdomo-Celis
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, UdeA, Medellín, Colombia
| | - Paula A. Velilla
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, UdeA, Medellín, Colombia
| | - Natalia A. Taborda
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, UdeA, Medellín, Colombia
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de la Salud, Corporación Universitaria Remington, Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, UdeA, Medellín, Colombia
- * E-mail:
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