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Alvarez I, Collado JA, Colobran R, Carrascal M, Ciudad MT, Canals F, James EA, Kwok WW, Gärtner M, Kyewski B, Pujol-Borrell R, Jaraquemada D. Central T cell tolerance: Identification of tissue-restricted autoantigens in the thymus HLA-DR peptidome. J Autoimmun 2015; 60:12-9. [PMID: 25911201 DOI: 10.1016/j.jaut.2015.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/12/2015] [Accepted: 03/18/2015] [Indexed: 11/22/2022]
Abstract
Promiscuous gene expression (pGE) of tissue-restricted self-antigens (TRA) in medullary thymic epithelial cells (mTECs) is in part driven by the Autoimmune Regulator gene (AIRE) and essential for self-tolerance. The link between AIRE functional mutations and multi-organ autoimmunity in human and mouse supports the role of pGE. Deep sequencing of the transcriptome revealed that mouse mTECs potentially transcribe an unprecedented range of >90% of all genes. Yet, it remains unclear to which extent these low-level transcripts are actually translated into proteins, processed and presented by thymic APCs to induce tolerance. To address this, we analyzed the HLA-DR-associated thymus peptidome. Within a large panel of peptides from abundant proteins, two TRA peptides were identified: prostate-specific semenogelin-1 (an autoantigen in autoimmune chronic prostatitis/chronic pelvic pain syndrome) and central nervous system-specific contactin-2 (an autoantigen in multiple sclerosis). Thymus expression of both genes was restricted to mTECs. SEMG1 expression was confined to mature HLA-DR(hi) mTECs of male and female donors and was AIRE-dependent, whereas CNTN2 was apparently AIRE-independent and was expressed by both populations of mTECs. Our findings establish a link between pGE, MHC-II peptide presentation and autoimmunity for bona fide human TRAs.
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Affiliation(s)
- Iñaki Alvarez
- Immunology Unit, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Javier A Collado
- Immunology Unit, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Roger Colobran
- Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08023 Barcelona, Spain
| | - Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Teresa Ciudad
- Immunology Unit, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Françesc Canals
- Proteomics Laboratory, Medical Oncology Research Program, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Martina Gärtner
- Division of Developmental Immunology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Bruno Kyewski
- Division of Developmental Immunology, Tumor Immunology Program, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Ricardo Pujol-Borrell
- Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Passeig Vall d'Hebron 119-129, 08023 Barcelona, Spain
| | - Dolores Jaraquemada
- Immunology Unit, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; Dept of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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52
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van Heemst J, Jansen DTSL, Polydorides S, Moustakas AK, Bax M, Feitsma AL, Bontrop-Elferink DG, Baarse M, van der Woude D, Wolbink GJ, Rispens T, Koning F, de Vries RRP, Papadopoulos GK, Archontis G, Huizinga TW, Toes RE. Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis. Nat Commun 2015; 6:6681. [PMID: 25942574 DOI: 10.1038/ncomms7681] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/18/2015] [Indexed: 01/09/2023] Open
Abstract
The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA)(+) rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we identify (citrullinated) vinculin, present in the joints of ACPA(+) RA patients, as an autoantigen targeted by ACPA and CD4(+) T cells. These T cells recognize an epitope with the core sequence DERAA, which is also found in many microbes and in protective HLA-DRB1*13 molecules, presented by predisposing HLA-DQ molecules. Moreover, these T cells crossreact with vinculin-derived and microbial-derived DERAA epitopes. Intriguingly, DERAA-directed T cells are not detected in HLA-DRB1*13(+) donors, indicating that the DERAA epitope from HLA-DRB1*13 mediates (thymic) tolerance in these donors and explaining the protective effects associated with HLA-DRB1*13. Together our data indicate the involvement of pathogen-induced DERAA-directed T cells in the HLA-RA association and provide a molecular basis for the contribution of protective/predisposing HLA alleles.
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Affiliation(s)
- Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Diahann T S L Jansen
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | | | - Antonis K Moustakas
- Faculty of Agricultural Technology, Technological Educational Institute of Ioanian Islands, Argostoli, Cephallonia 28100, Greece
| | - Marieke Bax
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Anouk L Feitsma
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Diënne G Bontrop-Elferink
- Department of Immunohematology and Bloodtransfusion, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Martine Baarse
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Diane van der Woude
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Gert-Jan Wolbink
- Sanquin Research and Landsteiner Laboratory, Academic Medical Center, 1066 CX Amsterdam, The Netherlands
| | - Theo Rispens
- Sanquin Research and Landsteiner Laboratory, Academic Medical Center, 1066 CX Amsterdam, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Bloodtransfusion, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - René R P de Vries
- Department of Immunohematology and Bloodtransfusion, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - George K Papadopoulos
- Laboratory of Biochemistry and Biophysics, Faculty of Agricultural Technology, Epirus Institute of Technology, Arta 47100, Greece
| | | | - Tom W Huizinga
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - René E Toes
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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53
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The ins and outs of MHC class II-mediated antigen processing and presentation. Nat Rev Immunol 2015; 15:203-16. [PMID: 25720354 DOI: 10.1038/nri3818] [Citation(s) in RCA: 650] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antigenic peptide-loaded MHC class II molecules (peptide-MHC class II) are constitutively expressed on the surface of professional antigen-presenting cells (APCs), including dendritic cells, B cells, macrophages and thymic epithelial cells, and are presented to antigen-specific CD4(+) T cells. The mechanisms of antigen uptake, the nature of the antigen processing compartments and the lifetime of cell surface peptide-MHC class II complexes can vary depending on the type of APC. It is likely that these differences are important for the function of each distinct APC subset in the generation of effective adaptive immune responses. In this Review, we describe our current knowledge of the mechanisms of uptake and processing of antigens, the intracellular formation of peptide-MHC class II complexes, the intracellular trafficking of peptide-MHC class II complexes to the APC plasma membrane and their ultimate degradation.
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Rodriguez SN, Jiang M, Bujo H, Allen PM. Self-pMHCII complexes are variably expressed in the thymus and periphery independent of mRNA expression but dependent on the activation state of the APCs. Mol Immunol 2015; 63:428-36. [PMID: 25451972 PMCID: PMC4254551 DOI: 10.1016/j.molimm.2014.09.016] [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: 08/18/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/23/2022]
Abstract
Self-peptide MHCII ligands are critical for selection of CD4+ T cells in the thymus, and maintenance in the periphery. To date, no investigation as to the exact thymic and peripheral expression of a naturally occurring positive selecting self-peptide MHCII (self-pMHCII) complex has taken place. We have generated a sensitive T cell hybridoma to functionally detect the endogenous presentation of a confirmed positive selecting self-pMHCII complex for a CD4+ transgenic T cell. Using this tool to survey and quantify the expression selecting of self-pMHCII, we have shown unequivocal proof that a known CD4+ selecting ligand can be presented on both positive and negative selecting thymic APCs. We also show that peripheral presentation of this same selecting ligand is affected by the activation state of the APCs. Furthermore, discrepancies between the gene expression and self-pMHCII complex presentation of this bona fide selecting ligand suggest that functional detection self-ligand complexes will be required to establish a complete view of the naturally presented endogenous self-pMHC landscape.
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Affiliation(s)
- Stephanie N Rodriguez
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Meizi Jiang
- Department of Clinical-Laboratory and Experimental-Research Medicine, Toho University, Sakura Medical Center, Sakura, Japan
| | - Hideaki Bujo
- Department of Clinical-Laboratory and Experimental-Research Medicine, Toho University, Sakura Medical Center, Sakura, Japan
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, United States.
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55
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The nature of self for T cells-a systems-level perspective. Curr Opin Immunol 2014; 34:1-8. [PMID: 25466393 DOI: 10.1016/j.coi.2014.10.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 10/28/2014] [Indexed: 11/24/2022]
Abstract
T-cell development and function are regulated by MHC-associated self peptides, collectively referred to as the immunopeptidome. Large-scale mass spectrometry studies have highlighted three key features of the immunopeptidome. First, it is not a mirror of the proteome or the transcriptome, and its content cannot be predicted with currently available bioinformatic tools. Second, the immunopeptidome is more plastic than previously anticipated, and is molded by several cell-intrinsic and cell-extrinsic factors. Finally, the complexity of the immunopeptidome goes beyond the 20-amino acids alphabet encoded in the germline, and is not restricted to canonical reading frames. The large amounts of 'dark matter' in the immunopeptidome, such as polymorphic, cryptic and mutant peptides, can now be explored using novel proteogenomic approaches that combine mass spectrometry and next-generation sequencing.
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56
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Chemotherapy enhances cross-presentation of nuclear tumor antigens. PLoS One 2014; 9:e107894. [PMID: 25243472 PMCID: PMC4171494 DOI: 10.1371/journal.pone.0107894] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/23/2014] [Indexed: 02/01/2023] Open
Abstract
Cross-presentation of tumor antigen is essential for efficient priming of naïve CD8+ T lymphocytes and induction of effective anti-tumor immunity. We hypothesized that the subcellular location of a tumor antigen could affect the efficiency of cross-presentation, and hence the outcome of anti-tumor responses to that antigen. We compared cross-presentation of a nominal antigen expressed in the nuclear, secretory, or cytoplasmic compartments of B16 melanoma tumors. All tumors expressed similar levels of the antigen. The antigen was cross-presented from all compartments but when the concentration was low, nuclear antigen was less efficiently cross-presented than antigen from other cellular locations. The efficiency of cross-presentation of the nuclear antigen was improved following chemotherapy-induced tumor cell apoptosis and this correlated with an increase in the proportion of effector CTL. These data demonstrate that chemotherapy improves nuclear tumor antigen cross-presentation and could be important for anti-cancer immunotherapies that target nuclear antigens.
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57
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Klein L, Kyewski B, Allen PM, Hogquist KA. Positive and negative selection of the T cell repertoire: what thymocytes see (and don't see). Nat Rev Immunol 2014; 14:377-91. [PMID: 24830344 PMCID: PMC4757912 DOI: 10.1038/nri3667] [Citation(s) in RCA: 889] [Impact Index Per Article: 88.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fate of developing T cells is specified by the interaction of their antigen receptors with self-peptide-MHC complexes that are displayed by thymic antigen-presenting cells (APCs). Various subsets of thymic APCs are strategically positioned in particular thymic microenvironments and they coordinate the selection of a functional and self-tolerant T cell repertoire. In this Review, we discuss the different strategies that these APCs use to sample and process self antigens and to thereby generate partly unique, 'idiosyncratic' peptide-MHC ligandomes. We discuss how the particular composition of the peptide-MHC ligandomes that are presented by specific APC subsets not only shapes the T cell repertoire in the thymus but may also indelibly imprint the behaviour of mature T cells in the periphery.
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Affiliation(s)
- Ludger Klein
- Institute for Immunology, Ludwig Maximilians University, 80336 Munich, Germany
| | - Bruno Kyewski
- Division of Developmental Immunology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55414, USA
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Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Nat Commun 2014; 5:3600. [PMID: 24714562 PMCID: PMC3996541 DOI: 10.1038/ncomms4600] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/10/2014] [Indexed: 12/23/2022] Open
Abstract
For decades, the global impact of genomic polymorphisms on the repertoire of peptides presented by major histocompatibility complex (MHC) has remained a matter of speculation. Here we present a novel approach that enables high-throughput discovery of polymorphic MHC class I-associated peptides (MIPs), which play a major role in allorecognition. On the basis of comprehensive analyses of the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings, we show that 0.5% of non-synonymous single nucleotide variations are represented in the MIP repertoire. The 34 polymorphic MIPs found in our subjects are encoded by bi-allelic loci with dominant and recessive alleles. Our analyses show that, at the population level, 12% of the MIP-coding exome is polymorphic. Our method provides fundamental insights into the relationship between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens). Mass spectrometry (MS) has furthered our understanding of MHC class I-associated peptides (MIPs), but the technique is inadequate for studying MIP-associated polymorphisms. Here, the authors combine high-throughput MS with exome and transcriptome sequencing to identify polymorphic MIPs from two female siblings.
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59
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Collado JA, Guitart C, Ciudad MT, Alvarez I, Jaraquemada D. The Repertoires of Peptides Presented by MHC-II in the Thymus and in Peripheral Tissue: A Clue for Autoimmunity? Front Immunol 2013; 4:442. [PMID: 24381570 PMCID: PMC3865459 DOI: 10.3389/fimmu.2013.00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/26/2013] [Indexed: 11/13/2022] Open
Abstract
T-cell tolerance to self-antigens is established in the thymus through the recognition by developing thymocytes of self-peptide-MHC complexes and induced and maintained in the periphery. Efficient negative selection of auto-reactive T cells in the thymus is dependent on the in situ expression of both ubiquitous and tissue-restricted self-antigens and on the presentation of derived peptides. Weak or inadequate intrathymic expression of self-antigens increases the risk to generate an autoimmune-prone T-cell repertoire. Indeed, even small changes of self-antigen expression in the thymus affect negative selection and increase the predisposition to autoimmunity. Together with other mechanisms, tolerance is maintained in the peripheral lymphoid organs via the recognition by mature T cells of a similar set of self-peptides in homeostatic conditions. However, non-lymphoid peripheral tissue, where organ-specific autoimmunity takes place, often have differential functional processes that may lead to the generation of epitopes that are absent or non-presented in the thymus. These putative differences between peptides presented by MHC molecules in the thymus and in peripheral tissues might be a major key to the initiation and maintenance of autoimmune conditions.
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Affiliation(s)
- Javier A Collado
- Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , Barcelona , Spain
| | - Carolina Guitart
- Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , Barcelona , Spain
| | - M Teresa Ciudad
- Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , Barcelona , Spain
| | - Iñaki Alvarez
- Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , Barcelona , Spain
| | - Dolores Jaraquemada
- Department of Cell Biology, Physiology and Immunology, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona , Barcelona , Spain
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60
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Stoeckle C, Rota IA, Tolosa E, Haller C, Melms A, Adamopoulou E. Isolation of myeloid dendritic cells and epithelial cells from human thymus. J Vis Exp 2013:e50951. [PMID: 24084687 DOI: 10.3791/50951] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In this protocol we provide a method to isolate dendritic cells (DC) and epithelial cells (TEC) from the human thymus. DC and TEC are the major antigen presenting cell (APC) types found in a normal thymus and it is well established that they play distinct roles during thymic selection. These cells are localized in distinct microenvironments in the thymus and each APC type makes up only a minor population of cells. To further understand the biology of these cell types, characterization of these cell populations is highly desirable but due to their low frequency, isolation of any of these cell types requires an efficient and reproducible procedure. This protocol details a method to obtain cells suitable for characterization of diverse cellular properties. Thymic tissue is mechanically disrupted and after different steps of enzymatic digestion, the resulting cell suspension is enriched using a Percoll density centrifugation step. For isolation of myeloid DC (CD11c(+)), cells from the low-density fraction (LDF) are immunoselected by magnetic cell sorting. Enrichment of TEC populations (mTEC, cTEC) is achieved by depletion of hematopoietic (CD45(hi)) cells from the low-density Percoll cell fraction allowing their subsequent isolation via fluorescence activated cell sorting (FACS) using specific cell markers. The isolated cells can be used for different downstream applications.
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Affiliation(s)
- Christina Stoeckle
- Department of General Neurology, Hertie Institute for Clinical Brain Research
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