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Pham HN, Pham L, Sato K. Deconvolution analysis identified altered hepatic cell landscape in primary sclerosing cholangitis and primary biliary cholangitis. Front Med (Lausanne) 2024; 11:1327973. [PMID: 38818402 PMCID: PMC11138208 DOI: 10.3389/fmed.2024.1327973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are characterized by ductular reaction, hepatic inflammation, and liver fibrosis. Hepatic cells are heterogeneous, and functional roles of different hepatic cell phenotypes are still not defined in the pathophysiology of cholangiopathies. Cell deconvolution analysis estimates cell fractions of different cell phenotypes in bulk transcriptome data, and CIBERSORTx is a powerful deconvolution method to estimate cell composition in microarray data. CIBERSORTx performs estimation based on the reference file, which is referred to as signature matrix, and allows users to create custom signature matrix to identify specific phenotypes. In the current study, we created two custom signature matrices using two single cell RNA sequencing data of hepatic cells and performed deconvolution for bulk microarray data of liver tissues including PSC and PBC patients. Methods Custom signature matrix files were created using single-cell RNA sequencing data downloaded from GSE185477 and GSE115469. Custom signature matrices were validated for their deconvolution performance using validation data sets. Cell composition of each hepatic cell phenotype in the liver, which was identified in custom signature matrices, was calculated by CIBERSORTx and bulk RNA sequencing data of GSE159676. Deconvolution results were validated by analyzing marker expression for the cell phenotype in GSE159676 data. Results CIBERSORTx and custom signature matrices showed comprehensive performance in estimation of population of various hepatic cell phenotypes. We identified increased population of large cholangiocytes in PSC and PBC livers, which is in agreement with previous studies referred to as ductular reaction, supporting the effectiveness and reliability of deconvolution analysis in this study. Interestingly, we identified decreased population of small cholangiocytes, periportal hepatocytes, and interzonal hepatocytes in PSC and PBC liver tissues compared to healthy livers. Discussion Although further studies are required to elucidate the roles of these hepatic cell phenotypes in cholestatic liver injury, our approach provides important implications that cell functions may differ depending on phenotypes, even in the same cell type during liver injury. Deconvolution analysis using CIBERSORTx could provide a novel approach for studies of specific hepatic cell phenotypes in liver diseases.
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Affiliation(s)
- Hoang Nam Pham
- Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Linh Pham
- Department of Science and Mathematics, Texas A&M University—Central Texas, Killeen, TX, United States
| | - Keisaku Sato
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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Ustiuzhanina MO, Streltsova MA, Timofeev ND, Kryukov MA, Chudakov DM, Kovalenko EI. Autologous T-Cell-Free Antigen Presentation System Unveils hCMV-Specific NK Cell Response. Cells 2024; 13:530. [PMID: 38534374 DOI: 10.3390/cells13060530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
NK cells play a decisive role in controlling hCMV infection by combining innate and adaptive-like immune reactions. The hCMV-derived VMAPRTLFL (LFL) peptide is a potent activator of NKG2C+ NK cells. Proposed here is an autologous system of LFL stimulation without T lymphocytes and exogenous cytokines that allows us to evaluate NK-cell hCMV-specific responses in more native settings. In this model, we evaluated LFL-induced IFNγ production, focusing on signaling pathways and the degranulation and proliferation of NK cells orchestrated by microenvironment cytokine production and analyzed the transcriptome of expanded NK cells. NK cells of individuals having high anti-hCMV-IgG levels, in contrast to NK cells of hCMV-seronegative and low-positive donors, displayed increased IFNγ production and degranulation and activation levels and enhanced proliferation upon LFL stimulation. Cytokine profiles of these LFL-stimulated cultures demonstrated a proinflammatory shift. LFL-induced NK-cell IFNγ production was dependent on the PI3K and Ras/Raf/Mek signaling pathways, independently of cytokines. In hCMV-seropositive individuals, this model allowed obtaining NK-cell antigen-specific populations proliferating in response to LFL. The transcriptomic profile of these expanded NK cells showed increased adaptive gene expression and metabolic activation. The results complement the existing knowledge about hCMV-specific NK-cell response. This model may be further exploited for the identification and characterization of antigen-specific NK cells.
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Affiliation(s)
- Maria O Ustiuzhanina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria A Streltsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikita D Timofeev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim A Kryukov
- Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Central European Institute of Technology, Masaryk University, 60200 Brno, Czech Republic
- Abu Dhabi Stem Cells Center, Abu Dhabi, United Arab Emirates
| | - Elena I Kovalenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Vojdani A, Koksoy S, Vojdani E, Engelman M, Benzvi C, Lerner A. Natural Killer Cells and Cytotoxic T Cells: Complementary Partners against Microorganisms and Cancer. Microorganisms 2024; 12:230. [PMID: 38276215 PMCID: PMC10818828 DOI: 10.3390/microorganisms12010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Natural killer (NK) cells and cytotoxic T (CD8+) cells are two of the most important types of immune cells in our body, protecting it from deadly invaders. While the NK cell is part of the innate immune system, the CD8+ cell is one of the major components of adaptive immunity. Still, these two very different types of cells share the most important function of destroying pathogen-infected and tumorous cells by releasing cytotoxic granules that promote proteolytic cleavage of harmful cells, leading to apoptosis. In this review, we look not only at NK and CD8+ T cells but also pay particular attention to their different subpopulations, the immune defenders that include the CD56+CD16dim, CD56dimCD16+, CD57+, and CD57+CD16+ NK cells, the NKT, CD57+CD8+, and KIR+CD8+ T cells, and ILCs. We examine all these cells in relation to their role in the protection of the body against different microorganisms and cancer, with an emphasis on their mechanisms and their clinical importance. Overall, close collaboration between NK cells and CD8+ T cells may play an important role in immune function and disease pathogenesis. The knowledge of how these immune cells interact in defending the body against pathogens and cancers may help us find ways to optimize their defensive and healing capabilities with methods that can be clinically applied.
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Affiliation(s)
- Aristo Vojdani
- Immunosciences Laboratory, Inc., Los Angeles, CA 90035, USA
| | - Sadi Koksoy
- Cyrex Laboratories, LLC, Phoenix, AZ 85034, USA; (S.K.); (M.E.)
| | | | - Mark Engelman
- Cyrex Laboratories, LLC, Phoenix, AZ 85034, USA; (S.K.); (M.E.)
| | - Carina Benzvi
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel; (C.B.); (A.L.)
| | - Aaron Lerner
- Chaim Sheba Medical Center, The Zabludowicz Research Center for Autoimmune Diseases, Ramat Gan 52621, Israel; (C.B.); (A.L.)
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Cross-Najafi AA, Farag K, Isidan A, Li W, Zhang W, Lin Z, Walsh JR, Lopez K, Park Y, Higgins NG, Cooper DK, Ekser B, Li P. Co-expression of HLA-E and HLA-G on genetically modified porcine endothelial cells attenuates human NK cell-mediated degranulation. Front Immunol 2023; 14:1217809. [PMID: 37529053 PMCID: PMC10387534 DOI: 10.3389/fimmu.2023.1217809] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Natural killer (NK) cells play an important role in immune rejection in solid organ transplantation. To mitigate human NK cell activation in xenotransplantation, introducing inhibitory ligands on xenografts via genetic engineering of pigs may protect the graft from human NK cell-mediated cytotoxicity and ultimately improve xenograft survival. In this study, non-classical HLA class I molecules HLA-E and HLA-G were introduced in an immortalized porcine liver endothelial cell line with disruption of five genes (GGTA1, CMAH, β4galNT2, SLA-I α chain, and β-2 microglobulin) encoding three major carbohydrate xenoantigens (αGal, Neu5Gc, and Sda) and swine leukocyte antigen class I (SLA-I) molecules. Expression of HLA-E and/or HLA-G on pig cells were confirmed by flow cytometry. Endogenous HLA-G molecules as well as exogenous HLA-G VL9 peptide could dramatically enhance HLA-E expression on transfected pig cells. We found that co-expression of HLA-E and HLA-G on porcine cells led to a significant reduction in human NK cell activation compared to the cells expressing HLA-E or HLA-G alone and the parental cell line. NK cell activation was assessed by analysis of CD107a expression in CD3-CD56+ population gated from human peripheral blood mononuclear cells. CD107a is a sensitive marker of NK cell activation and correlates with NK cell degranulation and cytotoxicity. HLA-E and/or HLA-G on pig cells did not show reactivity to human sera IgG and IgM antibodies. This in vitro study demonstrated that co-expression of HLA-E and HLA-G on genetically modified porcine endothelial cells provided a superior inhibition in human xenoreactive NK cells, which may guide further genetic engineering of pigs to prevent human NK cell mediated rejection.
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Affiliation(s)
- Arthur A. Cross-Najafi
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kristine Farag
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Abdulkadir Isidan
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Wei Li
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Wenjun Zhang
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Zhansong Lin
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Julia R. Walsh
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kevin Lopez
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yujin Park
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nancy G. Higgins
- Transplant Immunology, Indiana University Health, Indianapolis, IN, United States
| | - David K.C. Cooper
- Center for Transplantation Sciences, Massachusetts General Hospital/Harvard Medical School, Cambridge, MA, United States
| | - Burcin Ekser
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ping Li
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
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Savchenko AA, Kudryavtsev IV, Isakov DV, Sadowski IS, Belenyuk VD, Borisov AG. Recombinant Human Interleukin-2 Corrects NK Cell Phenotype and Functional Activity in Patients with Post-COVID Syndrome. Pharmaceuticals (Basel) 2023; 16:ph16040537. [PMID: 37111294 PMCID: PMC10144656 DOI: 10.3390/ph16040537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
Post-COVID syndrome develops in 10–20% of people who have recovered from COVID-19 and it is characterized by impaired function of the nervous, cardiovascular, and immune systems. Previously, it was found that patients who recovered from infection with the SARS-CoV-2 virus had a decrease in the number and functional activity of NK cells. The aim of the study was to assess the effectiveness of recombinant human IL-2 (rhIL-2) administered to correct NK cell phenotype and functional activity in patients with post-COVID syndrome. Patients were examined after 3 months for acute COVID-19 of varying severity. The phenotype of the peripheral blood NK cells was studied by flow cytometry. It was found that disturbances in the cell subset composition in patients with post-COVID syndrome were characterized by low levels of mature (p = 0.001) and cytotoxic NK cells (p = 0.013), with increased release of immature NK cells (p = 0.023). Functional deficiency of NK cells in post-COVID syndrome was characterized by lowered cytotoxic activity due to the decreased count of CD57+ (p = 0.001) and CD8+ (p < 0.001) NK cells. In the treatment of patients with post-COVID syndrome with recombinant IL-2, peripheral blood NK cell count and functional potential were restored. In general, the effectiveness of using rhIL-2 in treatment of post-COVID syndrome has been proven in patients with low levels of NK cells.
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Affiliation(s)
- Andrei A. Savchenko
- Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch of the Russian Academy of Sciences, Scientific Research Institute of Medical Problems of the North, 660022 Krasnoyarsk, Russia
| | - Igor V. Kudryavtsev
- Institute of Experimental Medicine, 197376 St. Petersburg, Russia
- School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Dmitry V. Isakov
- Institute of Experimental Medicine, Pavlov First St. Petersburg State Medical University of the Russian Federation Ministry of Healthcare, 197022 St. Petersburg, Russia
| | - Ivan S. Sadowski
- Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch of the Russian Academy of Sciences, Scientific Research Institute of Medical Problems of the North, 660022 Krasnoyarsk, Russia
| | - Vasily D. Belenyuk
- Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch of the Russian Academy of Sciences, Scientific Research Institute of Medical Problems of the North, 660022 Krasnoyarsk, Russia
| | - Alexandr G. Borisov
- Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch of the Russian Academy of Sciences, Scientific Research Institute of Medical Problems of the North, 660022 Krasnoyarsk, Russia
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Qin H, You C, Yan F, Tan K, Xu C, Zhao R, Ekpo MD, Tan S. Overcoming the challenges in translational development of natural killer cell therapeutics: An opinion paper. Front Oncol 2022; 12:1062765. [DOI: 10.3389/fonc.2022.1062765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
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