Early precursor T cells establish and propagate T cell exhaustion in chronic infection.
Animals
CD8-Positive T-Lymphocytes
/ immunology
Cell Differentiation
Cell Self Renewal
Cells, Cultured
Chronic Disease
Clonal Anergy
Epigenesis, Genetic
Hepatocyte Nuclear Factor 1-alpha
/ metabolism
Immune Tolerance
Lymphocytic Choriomeningitis
/ immunology
Lymphocytic choriomeningitis virus
/ physiology
Mice
Mice, Inbred C57BL
Mice, Transgenic
Precursor Cells, T-Lymphoid
/ immunology
Receptors, Antigen, T-Cell
/ metabolism
T-Cell Antigen Receptor Specificity
Journal
Nature immunology
ISSN: 1529-2916
Titre abrégé: Nat Immunol
Pays: United States
ID NLM: 100941354
Informations de publication
Date de publication:
10 2020
10 2020
Historique:
received:
13
03
2020
accepted:
10
07
2020
pubmed:
26
8
2020
medline:
7
1
2021
entrez:
26
8
2020
Statut:
ppublish
Résumé
CD8
Identifiants
pubmed: 32839610
doi: 10.1038/s41590-020-0760-z
pii: 10.1038/s41590-020-0760-z
doi:
Substances chimiques
Hepatocyte Nuclear Factor 1-alpha
0
Hnf1a protein, mouse
0
Receptors, Antigen, T-Cell
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1256-1266Références
McLane, L. M., Abdel-Hakeem, M. S. & Wherry, E. J. CD8 T cell exhaustion during chronic viral infection and cancer. Annu. Rev. Immunol. 37, 457–495 (2019).
pubmed: 30676822
doi: 10.1146/annurev-immunol-041015-055318
pmcid: 30676822
Hashimoto, M. et al. CD8 T cell exhaustion in chronic infection and cancer: opportunities for interventions. Annu. Rev. Med. 69, 301–318 (2018).
pubmed: 29414259
doi: 10.1146/annurev-med-012017-043208
pmcid: 29414259
Kuchroo, V. K., Anderson, A. C. & Petrovas, C. Coinhibitory receptors and CD8 T cell exhaustion in chronic infections. Curr. Opin. HIV AIDS 9, 439–445 (2014).
pubmed: 25010894
doi: 10.1097/COH.0000000000000088
pmcid: 25010894
Klebanoff, C. A., Gattinoni, L. & Restifo, N. P. CD8
pubmed: 16824130
pmcid: 1501075
doi: 10.1111/j.0105-2896.2006.00391.x
Baitsch, L. et al. Exhaustion of tumor-specific CD8
pubmed: 21555851
pmcid: 3104769
doi: 10.1172/JCI46102
Ahmadzadeh, M. et al. Tumor antigen–specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired. Blood 114, 1537–1544 (2009).
pubmed: 19423728
pmcid: 2927090
doi: 10.1182/blood-2008-12-195792
Lugli, E., Galletti, G., Boi, S. K. & Youngblood, B. A. Stem, effector, and hybrid states of memory CD8
pubmed: 31810790
doi: 10.1016/j.it.2019.11.004
pmcid: 31810790
Kallies, A., Zehn, D. & Utzschneider, D. T. Precursor exhausted T cells: key to successful immunotherapy? Nat. Rev. Immunol. 20, 128–136 (2020).
pubmed: 31591533
doi: 10.1038/s41577-019-0223-7
pmcid: 31591533
Utzschneider, D. T. et al. High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival. J. Exp. Med. 213, 1819–1834 (2016).
pubmed: 27455951
pmcid: 4995073
doi: 10.1084/jem.20150598
Angelosanto, J. M., Blackburn, S. D., Crawford, A. & Wherry, E. J. Progressive loss of memory T cell potential and commitment to exhaustion during chronic viral infection. J. Virol. 86, 8161–8170 (2012).
pubmed: 22623779
pmcid: 3421680
doi: 10.1128/JVI.00889-12
Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 571, 265–269 (2019).
pubmed: 31207605
doi: 10.1038/s41586-019-1326-9
Khan, O. et al. TOX transcriptionally and epigenetically programs CD8
pubmed: 31207603
pmcid: 6713202
doi: 10.1038/s41586-019-1325-x
Yao, C. et al. Single-cell RNA-seq reveals TOX as a key regulator of CD8
pubmed: 31209400
pmcid: 6588409
doi: 10.1038/s41590-019-0403-4
Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).
pubmed: 31207604
doi: 10.1038/s41586-019-1324-y
Seo, H. et al. TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8
pubmed: 31152140
doi: 10.1073/pnas.1905675116
Man, K. et al. Transcription factor IRF4 promotes CD8
doi: 10.1016/j.immuni.2017.11.021
Martinez, G. J. et al. The transcription factor NFAT promotes exhaustion of activated CD8
pubmed: 25680272
pmcid: 4346317
doi: 10.1016/j.immuni.2015.01.006
Wu, T. et al. The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness. Sci. Immunol. 1, eaai8593 (2016).
pubmed: 28018990
pmcid: 5179228
doi: 10.1126/sciimmunol.aai8593
Utzschneider, D. T. et al. T cell factor 1-expressing memory-like CD8
pubmed: 27533016
doi: 10.1016/j.immuni.2016.07.021
pmcid: 27533016
Im, S. J. et al. Defining CD8
pubmed: 27501248
pmcid: 5297183
doi: 10.1038/nature19330
He, R. et al. Follicular CXCR5-expressing CD8
pubmed: 27501245
doi: 10.1038/nature19317
pmcid: 27501245
Leong, Y. A. et al. CXCR5
pubmed: 27487330
doi: 10.1038/ni.3543
pmcid: 27487330
Hudson, W. H. et al. Proliferating transitory T cells with an effector-like transcriptional signature emerge from PD-1
pubmed: 31810882
doi: 10.1016/j.immuni.2019.11.002
pmcid: 31810882
Zander, R. et al. CD4
pubmed: 31810883
doi: 10.1016/j.immuni.2019.10.009
pmcid: 31810883
Miller, B. C. et al. Subsets of exhausted CD8
pubmed: 30778252
pmcid: 6673650
doi: 10.1038/s41590-019-0312-6
Sade-Feldman, M. et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 175, 998–1013.e20 (2018).
pubmed: 30388456
pmcid: 6641984
doi: 10.1016/j.cell.2018.10.038
Brummelman, J. et al. High-dimensional single cell analysis identifies stem-like cytotoxic CD8
pubmed: 30154266
pmcid: 6170179
doi: 10.1084/jem.20180684
Siddiqui, I. et al. Intratumoral Tcf1
pubmed: 30635237
doi: 10.1016/j.immuni.2018.12.021
Menner, A. J. et al. Id3 controls cell death of 2B4
pubmed: 26232435
doi: 10.4049/jimmunol.1402607
Kaech, S. M. & Wherry, E. J. Heterogeneity and cell-fate decisions in effector and memory CD8
pubmed: 17892848
pmcid: 3431921
doi: 10.1016/j.immuni.2007.08.007
Pauken, K. E. et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354, 1160–1165 (2016).
pubmed: 27789795
pmcid: 5484795
doi: 10.1126/science.aaf2807
Sen, D. R. et al. The epigenetic landscape of T cell exhaustion. Science 354, 1165–1169 (2016).
pubmed: 27789799
pmcid: 5497589
doi: 10.1126/science.aae0491
Oestreich, K. J., Yoon, H., Ahmed, R. & Boss, J. M. NFATc1 regulates PD-1 expression upon T cell activation. J. Immunol. 181, 4832–4839 (2008).
pubmed: 18802087
pmcid: 2645436
doi: 10.4049/jimmunol.181.7.4832
Lynn, R. C. et al. c-Jun overexpression in CAR T cells induces exhaustion resistance. Nature 576, 293–300 (2019).
pubmed: 31802004
pmcid: 31802004
doi: 10.1038/s41586-019-1805-z
Roychoudhuri, R. et al. BACH2 regulates CD8
pubmed: 27158840
pmcid: 4918801
doi: 10.1038/ni.3441
Sidwell, T. et al. Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis. Nat. Commun. 11, 252 (2020).
pubmed: 31937752
pmcid: 6959360
doi: 10.1038/s41467-019-14112-2
Wei, J. et al. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature 576, 471–476 (2019).
pubmed: 6937596
pmcid: 6937596
doi: 10.1038/s41586-019-1821-z
Xin, G. et al. A critical role of IL-21-induced BATF in sustaining CD8-T-cell-mediated chronic viral control. Cell Rep. 13, 1118–1124 (2015).
pubmed: 26527008
pmcid: 4859432
doi: 10.1016/j.celrep.2015.09.069
Grusdat, M. et al. IRF4 and BATF are critical for CD8
pubmed: 24531538
pmcid: 4207473
doi: 10.1038/cdd.2014.19
Utzschneider, D. T. et al. T cells maintain an exhausted phenotype after antigen withdrawal and population reexpansion. Nat. Immunol. 14, 603–610 (2013).
pubmed: 23644506
doi: 10.1038/ni.2606
pmcid: 23644506
Ghoneim, H. E. et al. De novo epigenetic programs inhibit PD-1 blockade-mediated T cell rejuvenation. Cell 170, 142–157.e19 (2017).
pubmed: 28648661
pmcid: 5568784
doi: 10.1016/j.cell.2017.06.007
Blank, C. U. et al. Defining ‘T cell exhaustion’. Nat. Rev. Immunol. 19, 665–674 (2019).
pubmed: 31570879
pmcid: 7286441
doi: 10.1038/s41577-019-0221-9
Chen, Z. et al. TCF-1-centered transcriptional network drives an effector versus exhausted CD8 T cell-fate decision. Immunity 51, 840–855.e5 (2019).
pubmed: 31606264
doi: 10.1016/j.immuni.2019.09.013
pmcid: 31606264
Diao, B. et al. Reduction and functional exhaustion of T cells in patients with coronavirus disease 2019 (COVID-19). Front. Immunol. 11, 827 (2020).
pubmed: 32425950
pmcid: 7205903
doi: 10.3389/fimmu.2020.00827
Miyazaki, M. et al. The opposing roles of the transcription factor E2A and its antagonist Id3 that orchestrate and enforce the naive fate of T cells. Nat. Immunol. 12, 992–1001 (2011).
pubmed: 21857655
pmcid: 3178719
doi: 10.1038/ni.2086
Kometani, K. et al. Repression of the transcription factor Bach2 contributes to predisposition of IgG1 memory B cells toward plasma cell differentiation. Immunity 39, 136–147 (2013).
pubmed: 23850379
doi: 10.1016/j.immuni.2013.06.011
pmcid: 23850379
Lee, P. P. et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763–774 (2001).
pubmed: 11728338
doi: 10.1016/S1074-7613(01)00227-8
pmcid: 11728338
Itoh-Nakadai, A. et al. The transcription repressors Bach2 and Bach1 promote B cell development by repressing the myeloid program. Nat. Immunol. 15, 1171–1180 (2014).
pubmed: 25344725
doi: 10.1038/ni.3024
pmcid: 25344725
Puglielli, M. T. et al. In vivo selection of a lymphocytic choriomeningitis virus variant that affects recognition of the GP33-43 epitope by H-2Db but not H-2Kb. J. Virol. 75, 5099–5107 (2001).
pubmed: 11333891
pmcid: 114915
doi: 10.1128/JVI.75.11.5099-5107.2001
Battegay, M. et al. Quantification of lymphocytic choriomeningitis virus with an immunological focus assay in 24- or 96-well plates. J. Virol. Methods 33, 191–198 (1991).
pubmed: 1939506
doi: 10.1016/0166-0934(91)90018-U
Blattman, J. N. et al. Estimating the precursor frequency of naive antigen-specific CD8 T cells. J. Exp. Med. 195, 657–664 (2002).
pubmed: 11877489
pmcid: 2193761
doi: 10.1084/jem.20001021
Liao, Y., Smyth, G. K. & Shi, W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).
pubmed: 23558742
pmcid: 3664803
doi: 10.1093/nar/gkt214
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
doi: 10.1093/bioinformatics/btt656
Liao, Y., Smyth, G. K. & Shi, W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 47, e47 (2019).
pubmed: 30783653
pmcid: 30783653
doi: 10.1093/nar/gkz114
Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15, R29 (2014).
pubmed: 24485249
pmcid: 4053721
doi: 10.1186/gb-2014-15-2-r29
Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
pubmed: 25605792
pmcid: 25605792
doi: 10.1093/nar/gkv007
McCarthy, D. J. & Smyth, G. K. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765–771 (2009).
pubmed: 19176553
pmcid: 2654802
doi: 10.1093/bioinformatics/btp053
Wu, D. et al. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics 26, 2176–2182 (2010).
pubmed: 20610611
pmcid: 2922896
doi: 10.1093/bioinformatics/btq401
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
pubmed: 24097267
pmcid: 3959825
doi: 10.1038/nmeth.2688
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432
pmcid: 2898526
doi: 10.1016/j.molcel.2010.05.004