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Flórez-Grau G, Escalona JC, Lacasta-Mambo H, Roelofs D, Bödder J, Beuk R, Schreibelt G, De Vries JIM. Human Dendritic Cell Subset Isolation by Magnetic Bead Sorting: A Protocol to Efficiently Obtain Pure Populations. Bio Protoc 2023; 13:e4851. [PMID: 37900109 PMCID: PMC10603258 DOI: 10.21769/bioprotoc.4851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/07/2023] [Accepted: 08/13/2023] [Indexed: 10/31/2023] Open
Abstract
Dendritic cells have been investigated for cell-based immunotherapy for various applications. The low abundance of dendritic cells in blood hampers their clinical application, resulting in the use of monocyte-derived dendritic cells as an alternative cell type. Limited knowledge is available regarding blood-circulating human dendritic cells, which can be divided into three subsets: type 2 conventional dendritic cells, type 1 conventional dendritic cells, and plasmacytoid dendritic cells. These subsets exhibit unique and desirable features for dendritic cell-based therapies. To enable efficient and reliable human research on dendritic cell subsets, we developed an efficient isolation protocol for the three human dendritic cell subsets, resulting in pure populations. The sequential steps include peripheral blood mononuclear cell isolation, magnetic-microbead lineage depletion (CD14, CD56, CD3, and CD19), and individual magnetic-microbead isolation of the three human dendritic cell subsets.
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Affiliation(s)
- Georgina Flórez-Grau
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jorge Cuenca Escalona
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helena Lacasta-Mambo
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daphne Roelofs
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johanna Bödder
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ruben Beuk
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Gerty Schreibelt
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolanda I. M. De Vries
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Del Prete A, Salvi V, Soriani A, Laffranchi M, Sozio F, Bosisio D, Sozzani S. Dendritic cell subsets in cancer immunity and tumor antigen sensing. Cell Mol Immunol 2023; 20:432-447. [PMID: 36949244 DOI: 10.1038/s41423-023-00990-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/14/2023] [Indexed: 03/24/2023] Open
Abstract
Dendritic cells (DCs) exhibit a specialized antigen-presenting function and play crucial roles in both innate and adaptive immune responses. Due to their ability to cross-present tumor cell-associated antigens to naïve T cells, DCs are instrumental in the generation of specific T-cell-mediated antitumor effector responses in the control of tumor growth and tumor cell dissemination. Within an immunosuppressive tumor microenvironment, DC antitumor functions can, however, be severely impaired. In this review, we focus on the mechanisms of DC capture and activation by tumor cell antigens and the role of the tumor microenvironment in shaping DC functions, taking advantage of recent studies showing the phenotype acquisition, transcriptional state and functional programs revealed by scRNA-seq analysis. The therapeutic potential of DC-mediated tumor antigen sensing in priming antitumor immunity is also discussed.
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Affiliation(s)
- Annalisa Del Prete
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Humanitas Clinical and Research Center-IRCCS Rozzano, Milano, Italy
| | - Valentina Salvi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Soriani
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Mattia Laffranchi
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesca Sozio
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Bosisio
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Silvano Sozzani
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
- IRCCS Neuromed, Pozzilli, IS, Italy.
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Mencarelli G, Pieroni B, Murphy KM, Gargaro M. Use of CRISPR/CAS9 Technologies to Study the Role of TLR in Dendritic Cell Subsets. Methods Mol Biol 2023; 2700:77-92. [PMID: 37603175 DOI: 10.1007/978-1-0716-3366-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Dendritic cells (DCs) have a significant role in coordinating both innate and adaptive immunity by serving as sentinels that detect invaders and initiate immune responses to eliminate them, as well as presenting antigens to activate adaptive immune responses that are specific to the antigen and the context in which it was detected. The regulation of DC functions is complex and involves intracellular drivers such as transcription factors and signaling pathways, as well as intercellular interactions with adhesion molecules, chemokines, and their receptors in the microenvironment. Toll-like receptors (TLRs) are crucial for DCs to detect pathogen-associated molecular patterns (PAMPs) and initiate downstream signaling pathways that lead to DC maturation and education in bridging with adaptive immunity, including the upregulation of MHC class II expression, induction of CD80, CD86, and CD40, and production of innate cytokines. Understanding the TLR pathways that DCs use to respond to innate immune stimuli and convert them into adaptive responses is important for new therapeutic targets identification.We present a novel platform that offers a fast and affordable CRISPR-Cas9 screening of genes that are involved in dendritic cells' TLR-dependent activation. Using CRISPR/Cas9 screening to target individual TLR genes in different dendritic cell subsets allows the identification of TLR-dependent pathways that regulate dendritic cell activation and cytokine production. This approach offers the efficient targeting of TLR driver genes to modulate the immune response and identify novel immune response regulators, establishing a causal link between these regulators and functional phenotypes based on genotypes.
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Affiliation(s)
- Giulia Mencarelli
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Benedetta Pieroni
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Marco Gargaro
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy.
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Rajamanickam A, Kumar NP, Pandiaraj AN, Selvaraj N, Munisankar S, Renji RM, Venkatramani V, Murhekar M, Thangaraj JWV, Kumar MS, Kumar CPG, Bhatnagar T, Ponnaiah M, Sabarinathan R, Saravanakumar V, Babu S. Restoration of dendritic cell homeostasis and Type I/Type III interferon levels in convalescent COVID-19 individuals. BMC Immunol 2022; 23:51. [PMID: 36289478 PMCID: PMC9607715 DOI: 10.1186/s12865-022-00526-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Plasmacytoid and myeloid dendritic cells play a vital role in the protection against viral infections. In COVID-19, there is an impairment of dendritic cell (DC) function and interferon secretion which has been correlated with disease severity. Results In this study, we described the frequency of DC subsets and the plasma levels of Type I (IFNα, IFNβ) and Type III Interferons (IFNλ1), IFNλ2) and IFNλ3) in seven groups of COVID-19 individuals, classified based on days since RT-PCR confirmation of SARS-CoV2 infection. Our data shows that the frequencies of pDC and mDC increase from Days 15–30 to Days 61–90 and plateau thereafter. Similarly, the levels of IFNα, IFNβ, IFNλ1, IFNλ2 and IFNλ3 increase from Days 15–30 to Days 61–90 and plateau thereafter. COVID-19 patients with severe disease exhibit diminished frequencies of pDC and mDC and decreased levels of IFNα, IFNβ, IFNλ1, IFNλ2 and IFNλ3. Finally, the percentages of DC subsets positively correlated with the levels of Type I and Type III IFNs. Conclusion Thus, our study provides evidence of restoration of homeostatic levels in DC subset frequencies and circulating levels of Type I and Type III IFNs in convalescent COVID-19 individuals. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-022-00526-z.
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Affiliation(s)
- Anuradha Rajamanickam
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
| | - Nathella Pavan Kumar
- grid.417330.20000 0004 1767 6138Immunology-ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu India
| | - Arul Nancy Pandiaraj
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
| | - Nandhini Selvaraj
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
| | - Saravanan Munisankar
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
| | - Rachel Mariam Renji
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
| | | | - Manoj Murhekar
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | | | - Muthusamy Santhosh Kumar
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | | | - Tarun Bhatnagar
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | - Manickam Ponnaiah
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | - Ramasamy Sabarinathan
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | - Velusamy Saravanakumar
- grid.419587.60000 0004 1767 6269ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu India
| | - Subash Babu
- grid.419685.7ICER-ICMR-NIRT-International Center for Excellence in Research, Chennai, Tamil Nadu India
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Woodberry T, Loughland JR, Minigo G. Whole Blood Dendritic Cell Cytokine Production Assay. Methods Mol Biol 2022; 2470:715-729. [PMID: 35881385 DOI: 10.1007/978-1-0716-2189-9_53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This protocol outlines a method for the timely detection of intracellular cytokines produced by activated dendritic cells (DC) in human whole blood. The quantification of cytokines is used to measure DC immune responsiveness, providing information on the breadth, strength, and DC subtypes responding spontaneously and to specific stimulation with toll-like receptor (TLR) ligands or parasite-infected erythrocytes. DC subsets, plasmacytoid DC, CD1c+ DC, CD141+ DC, and CD16+ DC, are examined in their natural environment of plasma and blood cells (erythrocytes, neutrophils, platelets, and leukocytes) enabling disease, medication, nutritional, and hematological effects on DC function to be examined in vaccine studies, ageing, health, and disease.
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Affiliation(s)
- Tonia Woodberry
- Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Jessica Rita Loughland
- Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gabriela Minigo
- Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
- College of Health and Human Sciences, Charles Darwin University, Darwin, NT, Australia.
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Naik SH. Dendritic cell development at a clonal level within a revised 'continuous' model of haematopoiesis. Mol Immunol 2020; 124:190-197. [PMID: 32593782 DOI: 10.1016/j.molimm.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022]
Abstract
Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid cells, has had a long and controversial history and is still not fully resolved. This review summarises the technological developments and findings that have been achieved at a clonal level, and how that has enhanced our knowledge of the process. It summarises the single cell lineage tracing technologies that have emerged, their application in in vitro and in vivo studies, in both mouse and human settings, and places the findings in a wider context of understanding haematopoiesis at a single cell or clonal level. In particular, it addresses the fate heterogeneity observed in many phenotypically defined progenitor subsets and how these findings have led to a departure from the classic ball-and-stick models of haematopoiesis to the emerging continuous model. Prior contradictions in DC development may be reconciled if they are framed within this revised model, where commitment to a lineage or cell type does not occur in an all-or-nothing process in defined progenitors but rather can occur at many stages of haematopoiesis in a dynamic process.
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Affiliation(s)
- Shalin H Naik
- Immunology Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia; The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
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7
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Soubéran A, Brustlein S, Gouarné C, Chasson L, Tchoghandjian A, Malissen M, Rougon G. Effects of VEGF blockade on the dynamics of the inflammatory landscape in glioblastoma-bearing mice. J Neuroinflammation 2019; 16:191. [PMID: 31660979 PMCID: PMC6816183 DOI: 10.1186/s12974-019-1563-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Targeting angiogenesis has been and continues to be an attractive therapeutic modality in glioblastoma (GBM) patients. However, GBM rapidly becomes refractory to anti-VEGF therapies. Myeloid cell infiltration is an important determinant of tumor progression. Given that VEGF is a modulator of the innate immune response we sought to analyze the dynamics of this response in a mouse model of GBM undergoing anti-VEGF therapy. METHODS We grafted GL261-DsRed cells in transgenic Thy1-CFP//LysM-EGFP//CD11c-EYFP reporter mice. We combined recurrent spectral two-photon imaging with multiparametric cytometry, immunostaining, and brain clearing to characterize at two critical stages of tumor development (day 21 and day 28 after tumor grafting) the nature and spatial distribution of the innate response in control and bevacizumab-treated mice. RESULTS We report that at an early stage (21 day), VEGF blockade has a detectable effect on the number of microglial cells but only a mild effect on the number of infiltrating myeloid cells. At a later stage (day 28), the treatment resulted in a specific adjustment of dendritic cell subsets. In treated mice, the number of monocytes and their monocyte-derived dendritic cells (moDC) progeny was increased by approximately twofold compared to untreated mice. In agreement, by in vivo quantitative imaging, we observed that treatment increased the number of LysM-EGFP cells traveling in tumor blood vessels and doubled the densities of both infiltrated LysM-EGFP monocytes and double-labeled EGFP/EYFP moDC. The treatment also led to an increased density of conventional cDCs2 subset together with a decrease of cDCs1 subset, necessary for the development of anti-tumor immunity. Finally, we describe differential spatial cell distributions and two immune cell-traveling routes into the brain. LysM-EGFP cells distributed as a gradient from the meninges towards the tumor whereas CD11c-EYFP/MHCII+ cells were located in the basal area of the tumor. Brain clearing also revealed a flow of CD11c-EYFP cells following the corpus callosum. CONCLUSION We uncovered new features in the dynamics of innate immune cells in GBM-bearing mice and deciphered precisely the key populations, i.e., DC subsets controlling immune responses, that are affected by VEGF blockade. Since despite differences, human pathogenesis presents similarities with our mouse model, the data provide new insights into the effect of bevacizumab at the cellular level.
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Affiliation(s)
- Aurélie Soubéran
- CNRS, Institut des Neurosciences de la Timone, UMR 7289, Aix-Marseille Univ, 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Sophie Brustlein
- CNRS, Institut des Neurosciences de la Timone, UMR 7289, Aix-Marseille Univ, 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Caroline Gouarné
- CNRS, Institut des Neurosciences de la Timone, UMR 7289, Aix-Marseille Univ, 27 Boulevard Jean Moulin, 13005, Marseille, France
| | - Lionel Chasson
- INSERM, CNRS Centre d'Immunologie de Marseille-Luminy, INSERM U1104, CNRS UMR7280, Aix-Marseille Univ, 13288, Marseille Cedex 9, France
| | - Aurélie Tchoghandjian
- CNRS, Institut de Neurophysiopathologie, UMR 7051, Aix-Marseille Univ, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marie Malissen
- INSERM, CNRS Centre d'Immunologie de Marseille-Luminy, INSERM U1104, CNRS UMR7280, Aix-Marseille Univ, 13288, Marseille Cedex 9, France
| | - Geneviève Rougon
- CNRS, Institut des Neurosciences de la Timone, UMR 7289, Aix-Marseille Univ, 27 Boulevard Jean Moulin, 13005, Marseille, France.
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Bouladoux N, Hennequin C, Malosse C, Malissen B, Belkaid Y, Henri S. Hapten-Specific T Cell-Mediated Skin Inflammation: Flow Cytometry Analysis of Mouse Skin Inflammatory Infiltrate. Methods Mol Biol 2017; 1559:21-36. [PMID: 28063034 DOI: 10.1007/978-1-4939-6786-5_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hapten-specific T cell-mediated skin inflammation also known as contact hypersensitivity (CHS) is characterized by a strong influx of CD8+ cytotoxic T cells within the skin upon reexposure of sensitized individuals to the same hapten. As many other leukocytes are also recruited during this elicitation phase, we attempted to revisit the skin infiltrate and characterize the inflammatory pattern. Recent improvement in the isolation in conventional as well as inflammatory dendritic cell and macrophage subsets from tissues and in the use of appropriate surface markers unraveling their heterogeneity should allow to determinate their specific functions in the CHS model. Here, we describe procedures to extract those cells from the skin and to analyze them by flow cytometry using a combination of appropriate surface markers allowing further transcriptomic analysis and functional assays.
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Sukriti S, Trehanpati N, Kumar M, Pande C, Hissar SS, Sarin SK. Functionally aberrant dendritic cell subsets and expression of DC-SIGN differentiate acute from chronic HBV infection. Hepatol Int 2016; 10:916-923. [PMID: 27658394 DOI: 10.1007/s12072-016-9763-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 08/22/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND Dendritic cells (DCs) promote pathogen recognition, uptake and presentation of antigen through DC-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and toll-like receptors (TLRs). AIMS AND OBJECTIVES We aimed to study temporal changes in DCs, TLRs and DC-SIGN during acute viral hepatitis B (AVHB) infection and compare them to chronic (CHB) and to investigate the earliest time point of activated pathogen recognition receptors in hepatitis B viral infection. METHODS We measured the frequencies of circulating myeloid (mDC) and plasmacytoid (pDC) dendritic cells and IFN-α production along with the expression of DC-SIGN and Toll Like Receptors (TLR's) in HBV patients at different time points. Also investigated in healthy volunteers, the dynamic changes in TLRs expression after receiving hepatitis B vaccine. RESULTS On follow-up of AVHB patients, we found the mDC population was significantly higher at week 4 and 6 (p < 0.02, 0.01), whereas the pDC population was unchanged at week 6 compared with week 0. Whereas frequencies of mDCs and pDCs were found to be elevated in AVHB and CHB patients than HC (p < 0.00 and 0.01, respectively) but was comparable among AVHB vs CHB. The DCs in CHB patients were functionally impaired with significantly low IFN-α production and low DCSIGN expression (p < 0.04 and 0.00, respectively). Even after stimulation by TLR agonists, no change was found in IFN-α production in CHB patients. MyD88 and IL-6, IFN-α mRNA levels were also found down-regulated. Interestingly, on follow-up after HBV vaccine, TLRs expression was found high at day 3 after vaccination. DISCUSSION The initial events of immune activation might be responsible for modulating immune response. These novel observations would pave the way for the development of antiviral strategies for chronic HBV infection.
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Affiliation(s)
- Sukriti Sukriti
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi, India
| | - Nirupma Trehanpati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi, India
| | - Manoj Kumar
- Department of Hepatology, Institute of Liver and Biliary Sciences, Delhi, India
| | - Chandana Pande
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi, India
| | - Syed S Hissar
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi, India
| | - Shiv Kumar Sarin
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi, India. .,Department of Hepatology, Institute of Liver and Biliary Sciences, Delhi, India.
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Abstract
Dendritic cells (DCs) are immune sentinels of the body and play a key role in the orchestration of the communication between the innate and the adaptive immune systems. DCs can polarize innate and adaptive immunity toward a variety of functions, sometimes with opposite roles in the overall control of immune responses (e.g., tolerance or immunosuppression versus immunity) or in the balance between various defense mechanisms promoting the control of different types of pathogens (e.g., antiviral versus antibacterial versus anti-worm immunity). These multiple DC functions result both from the plasticity of individual DC to exert different activities and from the existence of various DC subsets specialized in distinct functions. Functional genomics represents a powerful, unbiased, approach to better characterize these two levels of DC plasticity and to decipher its molecular regulation. Indeed, more and more experimental immunologists are generating high-throughput data in order to better characterize different states of DC based, for example, on their belonging to a specific subpopulation and/or on their exposure to specific stimuli and/or on their ability to exert a specific function. However, the interpretation of this wealth of data is severely hampered by the bottleneck of their bioinformatics analysis. Indeed, most experimental immunologists lack advanced computational or bioinformatics expertise and do not know how to translate raw gene expression data into potential biological meaning. Moreover, subcontracting such analyses is generally disappointing or financially not sustainable, since companies generally propose canonical analysis pipelines that are often unadapted for the structure of the data to analyze or for the precise type of questions asked. Hence, there is an important need of democratization of the bioinformatics analyses of gene expression profiling studies, in order to accelerate interpretation of the results by the researchers at the origin of the research project, of the data and who know best the underlying biology. This chapter will focus on the analysis of DC subset transcriptomes as measured by microarrays. We will show that simple bioinformatics procedures, applied one after the other in the framework of a pipeline, can lead to the characterization of DC subsets. We will develop two tutorials based on the reanalysis of public gene expression data. The first tutorial aims at illustrating a strategy for establishing the identity of DC subsets studied in a novel context, here their in vitro generation in cultures of human CD34(+) hematopoietic progenitors. The second tutorial aims at illustrating how to perform a posteriori bioinformatics analyses in order to evaluate the risk of contamination or of improper identification of DC subsets during preparation of biological samples, such that this information is taken into account in the final interpretation of the data and can eventually help to redesign the sampling strategy.
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Affiliation(s)
- Thien-Phong Vu Manh
- Centre d'Immunologie de Marseille-Luminy, UNIV UM2, Aix Marseille Université, 163 Avenue de Luminy, 13288, Marseille, France.
- U1104, INSERM, Marseille, France.
- UMR7280, CNRS, Marseille, France.
| | - Marc Dalod
- Centre d'Immunologie de Marseille-Luminy, UNIV UM2, Aix Marseille Université, 163 Avenue de Luminy, 13288, Marseille, France
- U1104, INSERM, Marseille, France
- UMR7280, CNRS, Marseille, France
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11
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Manh TPV, Alexandre Y, Baranek T, Crozat K, Dalod M. Plasmacytoid, conventional, and monocyte-derived dendritic cells undergo a profound and convergent genetic reprogramming during their maturation. Eur J Immunol 2013; 43:1706-15. [PMID: 23553052 PMCID: PMC3799015 DOI: 10.1002/eji.201243106] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/12/2013] [Accepted: 03/25/2013] [Indexed: 12/24/2022]
Abstract
DCs express receptors sensing microbial, danger or cytokine signals, which when triggered in combination drive DC maturation and functional polarization. Maturation was proposed to result from a discrete number of modifications in conventional DCs (cDCs), in contrast to a cell-fate conversion in plasmacytoid DCs (pDCs). cDC maturation is generally assessed by measuring cytokine production and membrane expression of MHC class II and co-stimulation molecules. pDC maturation complexity was demonstrated by functional genomics. Here, pDCs and cDCs were shown to undergo profound and convergent changes in their gene expression programs in vivo during viral infection. This observation was generalized to other stimulation conditions and DC subsets, by public microarray data analyses, PCR confirmation of selected gene expression profiles, and gene regulatory sequence bioinformatics analyses. Thus, maturation is a complex process similarly reshaping all DC subsets, including through the induction of a core set of NF-κB- or IFN-stimulated genes irrespective of stimuli.
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Affiliation(s)
- Thien-Phong Vu Manh
- Centre d'Immunologie de Marseille-Luminy, UNIV UM2, Aix-Marseille Université, Parc scientifique et technologique de Luminy, Marseille, France
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