Gene Expression-Based Identification of Antigen-Responsive CD8 + T Cells on a Single-Cell Level
CD8 T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8 T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-la...
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| Published in: | Frontiers in immunology Vol. 10; p. 2568 |
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| Main Authors: | , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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| Abstract | CD8
T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8
T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8
T cells under different antigen presentation conditions. Combined expression of
, and
was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8
T cells from unselected populations. Gene response profiles of CD8
T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors. |
|---|---|
| AbstractList | CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8+ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8+ T cells from unselected populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors. CD8 + T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8 + T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8 + T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2 , and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8 + T cells from unselected populations. Gene response profiles of CD8 + T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors. CD8 T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8 T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8 T cells under different antigen presentation conditions. Combined expression of , and was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8 T cells from unselected populations. Gene response profiles of CD8 T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors. |
| Author | Morgenstern, Robert Kraus, Gloria Bonifacio, Ezio Eugster, Anne Fuchs, Yannick F Sharma, Virag Reinhardt, Susanne Dahl, Andreas Lindner, Annett Petzold, Andreas Löbel, Doreen |
| AuthorAffiliation | 1 Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden , Dresden , Germany 2 German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden , Dresden , Germany 4 Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health , Neuherberg , Germany 3 DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden , Dresden , Germany |
| AuthorAffiliation_xml | – name: 1 Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden , Dresden , Germany – name: 2 German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden , Dresden , Germany – name: 4 Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health , Neuherberg , Germany – name: 3 DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden , Dresden , Germany |
| Author_xml | – sequence: 1 givenname: Yannick F surname: Fuchs fullname: Fuchs, Yannick F organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 2 givenname: Virag surname: Sharma fullname: Sharma, Virag organization: German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 3 givenname: Anne surname: Eugster fullname: Eugster, Anne organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 4 givenname: Gloria surname: Kraus fullname: Kraus, Gloria organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 5 givenname: Robert surname: Morgenstern fullname: Morgenstern, Robert organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 6 givenname: Andreas surname: Dahl fullname: Dahl, Andreas organization: DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany – sequence: 7 givenname: Susanne surname: Reinhardt fullname: Reinhardt, Susanne organization: DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany – sequence: 8 givenname: Andreas surname: Petzold fullname: Petzold, Andreas organization: DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany – sequence: 9 givenname: Annett surname: Lindner fullname: Lindner, Annett organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 10 givenname: Doreen surname: Löbel fullname: Löbel, Doreen organization: Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany – sequence: 11 givenname: Ezio surname: Bonifacio fullname: Bonifacio, Ezio organization: Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany |
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| Cites_doi | 10.1016/S0022-1759(01)00499-9 10.1084/jem.20111187 10.1038/nmeth.1345 10.1073/pnas.092141999 10.1126/science.273.5271.104 10.1038/nprot.2012.037 10.1126/sciimmunol.aao4013 10.4049/jimmunol.171.3.1542 10.1038/nature21379 10.1016/j.jim.2008.07.017 10.4049/jimmunol.0901248 10.1182/blood-2006-11-056168 10.1038/nature22383 10.1371/journal.pcbi.1003696 10.1093/intimm/dxh340 10.1073/pnas.1603106113 10.1016/j.celrep.2018.04.038 10.1186/1471-2164-9-225 10.1016/j.clim.2015.02.012 10.1073/pnas.1417215111 10.1016/j.immuni.2017.01.003 10.1038/nmeth.2967 10.1084/jem.20160553 10.4049/jimmunol.181.10.7407 10.4049/jimmunol.176.5.3257 10.1016/j.immuni.2012.12.006 10.3389/fimmu.2018.02775 10.1186/s13059-014-0550-8 10.1016/j.cmet.2018.07.007 10.1016/j.jim.2018.08.011 10.1038/ni.2687 10.1001/jama.2015.2928 10.1146/annurev-immunol-042617-053429 10.1371/journal.pone.0049213 10.1016/j.jaut.2011.05.012 10.1126/science.1258367 10.1007/978-1-61779-842-9_32 10.1038/srep44661 10.1111/j.1365-3083.2006.01879.x 10.4049/jimmunol.1801090 10.1038/nmeth.3800 10.1038/nature22976 10.3389/fimmu.2018.01378 10.1038/nbt.4096 10.1038/nprot.2014.006 |
| ContentType | Journal Article |
| Copyright | Copyright © 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio. Copyright © 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio. 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio |
| Copyright_xml | – notice: Copyright © 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio. – notice: Copyright © 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio. 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio |
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| Keywords | CD8+ T cells CMV pp65 antigen-responsive single-cell gene-expression analysis influenza matrix protein CTL (cytotoxic T lymphocyte) T cell receptor (TCR) |
| Language | English |
| License | Copyright © 2019 Fuchs, Sharma, Eugster, Kraus, Morgenstern, Dahl, Reinhardt, Petzold, Lindner, Löbel and Bonifacio. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Sid P. Kerkar, Boehringer Ingelheim, United States; Guo Fu, Xiamen University, China Edited by: Nick Gascoigne, National University of Singapore, Singapore These authors have contributed equally to this work ORCID: Andreas Dahl orcid.org/0000-0002-2668-8371 This article was submitted to T Cell Biology, a section of the journal Frontiers in Immunology |
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| References | Kao (B9) 2005; 17 Pan (B17) 2017; 543 Bonifacio (B39) 2015; 313 McDavid (B40) 2014; 10 Williams (B36) 2018; 462 Culina (B24) 2018; 3 Kharchenko (B41) 2014; 11 Valkenburg (B12) 2016; 113 Lippert (B31) 2003; 171 Gonzalez-Duque (B35) 2018; 28 Alamyar (B45) 2012; 882 Glanville (B4) 2017; 547 Fan (B6) 2015; 347 Brewitz (B15) 2017; 46 Matsuo (B25) 2018; 9 Roge (B33) 2007; 65 Wehler (B19) 2008; 339 Takeuchi (B16) 2009; 183 Alcover (B10) 2018; 36 Picelli (B38) 2014; 9 Hadrup (B3) 2009; 6 Stelekati (B30) 2018; 23 Love (B42) 2014; 15 Butler (B43) 2018; 36 Fuchs (B23) 2017; 7 Grifoni (B34) 2018; 201 Naumov (B13) 2008; 181 Dudda (B29) 2013; 38 Gubser (B32) 2013; 14 Fuchs (B14) 2015; 157 Wolfl (B18) 2007; 110 Takaki (B21) 2006; 176 Coppieters (B20) 2012; 209 Du (B28) 2014; 111 Britten (B37) 2002; 259 Wang (B8) 2008; 9 Miao (B27) 2017; 214 Viola (B11) 1996; 273 Dolton (B7) 2018; 9 Unger (B2) 2011; 37 Dash (B5) 2017; 547 Stubbington (B44) 2016; 13 Dorner (B26) 2002; 99 Andersen (B1) 2012; 7 Unger (B22) 2012; 7 |
| References_xml | – volume: 259 start-page: 95 year: 2002 ident: B37 article-title: The use of HLA-A*0201-transfected K562 as standard antigen-presenting cells for CD8(+) T lymphocytes in IFN-gamma ELISPOT assays publication-title: J Immunol Methods. doi: 10.1016/S0022-1759(01)00499-9 contributor: fullname: Britten – volume: 209 start-page: 51 year: 2012 ident: B20 article-title: Demonstration of islet-autoreactive CD8 T cells in insulitic lesions from recent onset and long-term type 1 diabetes patients publication-title: J Exp Med. doi: 10.1084/jem.20111187 contributor: fullname: Coppieters – volume: 6 start-page: 520 year: 2009 ident: B3 article-title: Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers publication-title: Nat Methods. doi: 10.1038/nmeth.1345 contributor: fullname: Hadrup – volume: 99 start-page: 6181 year: 2002 ident: B26 article-title: MIP-1alpha, MIP-1beta, RANTES, and ATAC/lymphotactin function together with IFN-gamma as type 1 cytokines publication-title: Proc Natl Acad Sci USA. doi: 10.1073/pnas.092141999 contributor: fullname: Dorner – volume: 273 start-page: 104 year: 1996 ident: B11 article-title: T cell activation determined by T cell receptor number and tunable thresholds publication-title: Science. doi: 10.1126/science.273.5271.104 contributor: fullname: Viola – volume: 7 start-page: 891 year: 2012 ident: B1 article-title: Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers publication-title: Nat Protoc. doi: 10.1038/nprot.2012.037 contributor: fullname: Andersen – volume: 3 start-page: eaao4013 year: 2018 ident: B24 article-title: Islet-reactive CD8(+) T cell frequencies in the pancreas, but not in blood, distinguish type 1 diabetic patients from healthy donors publication-title: Sci Immunol. doi: 10.1126/sciimmunol.aao4013 contributor: fullname: Culina – volume: 171 start-page: 1542 year: 2003 ident: B31 article-title: Role of regulator of G protein signaling 16 in inflammation-induced T lymphocyte migration and activation publication-title: J Immunol. doi: 10.4049/jimmunol.171.3.1542 contributor: fullname: Lippert – volume: 543 start-page: 252 year: 2017 ident: B17 article-title: Survival of tissue-resident memory T cells requires exogenous lipid uptake and metabolism publication-title: Nature. doi: 10.1038/nature21379 contributor: fullname: Pan – volume: 339 start-page: 23 year: 2008 ident: B19 article-title: Rapid identification and sorting of viable virus-reactive CD4(+) and CD8(+) T cells based on antigen-triggered CD137 expression publication-title: J Immunol Methods. doi: 10.1016/j.jim.2008.07.017 contributor: fullname: Wehler – volume: 183 start-page: 4220 year: 2009 ident: B16 article-title: CRTAM confers late-stage activation of CD8+ T cells to regulate retention within lymph node publication-title: J Immunol. doi: 10.4049/jimmunol.0901248 contributor: fullname: Takeuchi – volume: 110 start-page: 201 year: 2007 ident: B18 article-title: Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities publication-title: Blood. doi: 10.1182/blood-2006-11-056168 contributor: fullname: Wolfl – volume: 547 start-page: 89 year: 2017 ident: B5 article-title: Quantifiable predictive features define epitope-specific T cell receptor repertoires publication-title: Nature. doi: 10.1038/nature22383 contributor: fullname: Dash – volume: 10 start-page: e1003696 year: 2014 ident: B40 article-title: Modeling bi-modality improves characterization of cell cycle on gene expression in single cells publication-title: PLoS Computat Biol. doi: 10.1371/journal.pcbi.1003696 contributor: fullname: McDavid – volume: 17 start-page: 1607 year: 2005 ident: B9 article-title: Loss of CD8 and TCR binding to Class I MHC ligands following T cell activation publication-title: Int Immunol. doi: 10.1093/intimm/dxh340 contributor: fullname: Kao – volume: 113 start-page: 4440 year: 2016 ident: B12 article-title: Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses publication-title: Proc Natl Acad Sci USA. doi: 10.1073/pnas.1603106113 contributor: fullname: Valkenburg – volume: 23 start-page: 2142 year: 2018 ident: B30 article-title: Long-term persistence of exhausted CD8 T cells in chronic infection is regulated by MicroRNA-155 publication-title: Cell Rep. doi: 10.1016/j.celrep.2018.04.038 contributor: fullname: Stelekati – volume: 9 start-page: 225 year: 2008 ident: B8 article-title: Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-cell activation publication-title: BMC Genomics. doi: 10.1186/1471-2164-9-225 contributor: fullname: Wang – volume: 157 start-page: 216 year: 2015 ident: B14 article-title: Vagaries of the ELISpot assay: specific detection of antigen responsive cells requires purified CD8(+) T cells and MHC class I expressing antigen presenting cell lines publication-title: Clin Immunol. doi: 10.1016/j.clim.2015.02.012 contributor: fullname: Fuchs – volume: 111 start-page: 16484 year: 2014 ident: B28 article-title: EGR2 is critical for peripheral naive T-cell differentiation and the T-cell response to influenza publication-title: Proc Natl Acad Sci USA. doi: 10.1073/pnas.1417215111 contributor: fullname: Du – volume: 46 start-page: 205 year: 2017 ident: B15 article-title: CD8(+) T cells orchestrate pDC-XCR1(+) dendritic cell spatial and functional cooperativity to optimize priming publication-title: Immunity. doi: 10.1016/j.immuni.2017.01.003 contributor: fullname: Brewitz – volume: 11 start-page: 740 year: 2014 ident: B41 article-title: Bayesian approach to single-cell differential expression analysis publication-title: Nat Methods. doi: 10.1038/nmeth.2967 contributor: fullname: Kharchenko – volume: 214 start-page: 1787 year: 2017 ident: B27 article-title: Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation publication-title: J Exp Med. doi: 10.1084/jem.20160553 contributor: fullname: Miao – volume: 181 start-page: 7407 year: 2008 ident: B13 article-title: Multiple glycines in TCR alpha-chains determine clonally diverse nature of human T cell memory to influenza A virus publication-title: J Immunol. doi: 10.4049/jimmunol.181.10.7407 contributor: fullname: Naumov – volume: 176 start-page: 3257 year: 2006 ident: B21 article-title: HLA-A*0201-restricted T cells from humanized NOD mice recognize autoantigens of potential clinical relevance to type 1 diabetes publication-title: J Immunol. doi: 10.4049/jimmunol.176.5.3257 contributor: fullname: Takaki – volume: 38 start-page: 742 year: 2013 ident: B29 article-title: MicroRNA-155 is required for effector CD8+ T cell responses to virus infection and cancer publication-title: Immunity. doi: 10.1016/j.immuni.2012.12.006 contributor: fullname: Dudda – volume: 9 start-page: 2775 year: 2018 ident: B25 article-title: A highly active form of XCL1/Lymphotactin functions as an effective adjuvant to recruit cross-presenting dendritic cells for induction of effector and memory CD8(+) T cells publication-title: Front Immunol. doi: 10.3389/fimmu.2018.02775 contributor: fullname: Matsuo – volume: 15 start-page: 550 year: 2014 ident: B42 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 publication-title: Genome Biol. doi: 10.1186/s13059-014-0550-8 contributor: fullname: Love – volume: 28 start-page: 946 year: 2018 ident: B35 article-title: Conventional and neo-antigenic peptides presented by β cells are targeted by circulating naive CD8+ T cells in type 1 diabetic and healthy donors publication-title: Cell Metabo. doi: 10.1016/j.cmet.2018.07.007 contributor: fullname: Gonzalez-Duque – volume: 462 start-page: 65 year: 2018 ident: B36 article-title: Development of T cell lines sensitive to antigen stimulation publication-title: J Immunol Methods. doi: 10.1016/j.jim.2018.08.011 contributor: fullname: Williams – volume: 14 start-page: 1064 year: 2013 ident: B32 article-title: Rapid effector function of memory CD8+ T cells requires an immediate-early glycolytic switch publication-title: Nat Immunol. doi: 10.1038/ni.2687 contributor: fullname: Gubser – volume: 313 start-page: 1541 year: 2015 ident: B39 article-title: Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: the Pre-POINT randomized clinical trial publication-title: JAMA. doi: 10.1001/jama.2015.2928 contributor: fullname: Bonifacio – volume: 36 start-page: 103 year: 2018 ident: B10 article-title: Cell biology of T cell receptor expression and regulation publication-title: Ann Rev Immunol. doi: 10.1146/annurev-immunol-042617-053429 contributor: fullname: Alcover – volume: 7 start-page: e49213 year: 2012 ident: B22 article-title: Islet-specific CTL cloned from a type 1 diabetes patient cause beta-cell destruction after engraftment into HLA-A2 transgenic NOD/scid/IL2RG null mice publication-title: PLoS ONE. doi: 10.1371/journal.pone.0049213 contributor: fullname: Unger – volume: 37 start-page: 151 year: 2011 ident: B2 article-title: Discovery of low-affinity preproinsulin epitopes and detection of autoreactive CD8 T-cells using combinatorial MHC multimers publication-title: J Autoimmun. doi: 10.1016/j.jaut.2011.05.012 contributor: fullname: Unger – volume: 347 start-page: 1258367 year: 2015 ident: B6 article-title: Expression profiling. Combinatorial labeling of single cells for gene expression cytometry publication-title: Science. doi: 10.1126/science.1258367 contributor: fullname: Fan – volume: 882 start-page: 569 year: 2012 ident: B45 article-title: IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS publication-title: Methods Mol Biol. doi: 10.1007/978-1-61779-842-9_32 contributor: fullname: Alamyar – volume: 7 start-page: 44661 year: 2017 ident: B23 article-title: CD8(+) T cells specific for the islet autoantigen IGRP are restricted in their T cell receptor chain usage publication-title: Sci Rep. doi: 10.1038/srep44661 contributor: fullname: Fuchs – volume: 65 start-page: 202 year: 2007 ident: B33 article-title: Commonly used reference genes are actively regulated in in vitro stimulated lymphocytes publication-title: Scand J Immuno. doi: 10.1111/j.1365-3083.2006.01879.x contributor: fullname: Roge – volume: 201 start-page: 3487 year: 2018 ident: B34 article-title: Cutting edge: transcriptional profiling reveals multifunctional and cytotoxic antiviral responses of zika virus-specific CD8(+) T cells publication-title: J Immunol. doi: 10.4049/jimmunol.1801090 contributor: fullname: Grifoni – volume: 13 start-page: 329 year: 2016 ident: B44 article-title: T cell fate and clonality inference from single-cell transcriptomes publication-title: Nat Methods. doi: 10.1038/nmeth.3800 contributor: fullname: Stubbington – volume: 547 start-page: 94 year: 2017 ident: B4 article-title: Identifying specificity groups in the T cell receptor repertoire publication-title: Nature. doi: 10.1038/nature22976 contributor: fullname: Glanville – volume: 9 start-page: 1378 year: 2018 ident: B7 article-title: Optimized Peptide-MHC multimer protocols for detection and isolation of autoimmune T-cells publication-title: Front Immunol. doi: 10.3389/fimmu.2018.01378 contributor: fullname: Dolton – volume: 36 start-page: 411 year: 2018 ident: B43 article-title: Integrating single-cell transcriptomic data across different conditions, technologies, and species publication-title: Nat Biotechnol. doi: 10.1038/nbt.4096 contributor: fullname: Butler – volume: 9 start-page: 171 year: 2014 ident: B38 article-title: Full-length RNA-seq from single cells using Smart-seq2 publication-title: Nat Protoc. doi: 10.1038/nprot.2014.006 contributor: fullname: Picelli |
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T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8... CD8 + T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive... CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive... |
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| SubjectTerms | antigen-responsive CD8+ T cells CTL (cytotoxic T lymphocyte) gene-expression analysis Immunology influenza matrix protein single-cell |
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| Title | Gene Expression-Based Identification of Antigen-Responsive CD8 + T Cells on a Single-Cell Level |
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