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Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection
Open accessAbstract
Summary In response to acute infection, naive CD8+ T cells expand, differentiate into effector cells and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8+ T cells acquire an “exhausted” phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8+ T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq. Acquisition of effector, memory or exhausted phenotypes was associated with stable changes in chromatin accessibility away from the naive T cell state. Regions differentially-accessible between functional subsets in vivo were enriched for binding sites of transcription factors known to regulate these subsets, including E2A, BATF, IRF4, T-bet and TCF1. Exhaustion-specific accessible regions were enriched for consensus binding sites for NFAT and Nr4a family members, indicating that chronic stimulation confers a unique accessibility profile on exhausted cells.
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Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
The blockade of immune checkpoints in cancer immunotherapy
Pardoll, D. M. (2012) · Nature Reviews Cancer · doi:10.1038/nrc3239 · Cited by 13,838
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
Molecular and cellular insights into T cell exhaustion
Wherry, E. J., & Kurachi, M. (2015) · Nature Reviews Immunology · doi:10.1038/nri3862 · Cited by 4,652
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137
Wherry, E. J. (2011) · Nature Immunology · doi:10.1038/ni.2035 · Cited by 4,062 · cited 2×
“…or latent infection—as in mice or humans infectedwith LCMV clone 13, human immunode- ficiency virus, hepatitis B virus, or hepatitis C virus—CD8+ T cells often enter a state of unresponsiveness to further stimulation that has been termed ‘‘exhaustion’’ (Moskophidis et al., 1993; Wherry, 2011).”
BackgroundThe accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Lineage relationship and protective immunity of memory CD8 T cell subsets
Wherry, E. J., Teichgräber, V., Becker, T. C., Masopust, D., Kaech, S. M., Antia, R., von Andrian, U. H., & Ahmed, R. (2003) · Nature Immunology · doi:10.1038/ni889 · Cited by 1,864
Cited by
Chromatin accessibility and the regulatory epigenome
Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793
TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
Khan, O., Giles, J. R., McDonald, S., Manne, S., Ngiow, S. F., Patel, K. P., Werner, M. T., Huang, A. C., Alexander, K. A., Wu, J. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1325-x · Cited by 1,646
Blank, C. U., Haining, W. N., Held, W., Hogan, P. G., Kallies, A., Lugli, E., Lynn, R. C., Philip, M., Rao, A., Restifo, N. P., et al. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-019-0221-9 · Cited by 1,603
Self-citationTOX is a critical regulator of tumour-specific T cell differentiation
Scott, A. C., Dündar, F., Zumbo, P., Chandran, S. S., Klebanoff, C. A., Shakiba, M., Trivedi, P., Menocal, L., Appleby, H., Camara, S., et al. (2019) · Nature · doi:10.1038/s41586-019-1324-y · Cited by 1,106
Advances in the development of personalized neoantigen-based therapeutic cancer vaccines
Blass, E., & Ott, P. A. (2021) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-020-00460-2 · Cited by 1,042
Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0206-z · Cited by 980
Chromatin states define tumour-specific T cell dysfunction and reprogramming
Philip, M., Fairchild, L., Sun, L., Horste, E. L., Camara, S., Shakiba, M., Scott, A. C., Viale, A., Lauer, P., Merghoub, T., et al. (2017) · Nature · doi:10.1038/nature22367 · Cited by 933
Turning Cold into Hot: Firing up the Tumor Microenvironment
Duan, Q., Zhang, H., Zheng, J., & Zhang, L. (2020) · Trends in Cancer · doi:10.1016/j.trecan.2020.02.022 · Cited by 934
NR4A transcription factors limit CAR T cell function in solid tumours
Chen, J., López-Moyado, I. F., Seo, H., Lio, C.-W. J., Hempleman, L. J., Sekiya, T., Yoshimura, A., Scott-Browne, J. P., & Rao, A. (2019) · Nature · doi:10.1038/s41586-019-0985-x · Cited by 874
Self-citationSeo, H., Chen, J., González-Avalos, E., Samaniego-Castruita, D., Das, A., Wang, Y. H., López-Moyado, I. F., Georges, R. O., Zhang, W., Onodera, A., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1905675116 · Cited by 808
Self-citationCheckpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1-CD8+ Tumor-Infiltrating T Cells
Kurtulus, S., Madi, A., Escobar, G., Klapholz, M., Nyman, J., Christian, E., Pawlak, M., Dionne, D., Xia, J., Rozenblatt-Rosen, O., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.11.014 · Cited by 636
Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction
Liu, X., Wang, Y., Lu, H., Li, J., Yan, X., Xiao, M., Hao, J., Alekseev, A., Khong, H., Chen, T., et al. (2019) · Nature · doi:10.1038/s41586-019-0979-8 · Cited by 533
Baessler, A., & Vignali, D. A. A. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-090222-110914 · Cited by 420
Belk, J. A., Yao, W., Ly, N., Freitas, K. A., Chen, Y.-T., Shi, Q., Valencia, A. M., Shifrut, E., Kale, N., Yost, K. E., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.06.001 · Cited by 382
Dynamics and genomic landscape of CD8+ T cells undergoing hepatic priming
Bénéchet, A. P., De Simone, G., Di Lucia, P., Cilenti, F., Barbiera, G., Le Bert, N., Fumagalli, V., Lusito, E., Moalli, F., Bianchessi, V., et al. (2019) · Nature · doi:10.1038/s41586-019-1620-6 · Cited by 222
Pais Ferreira, D., Silva, J. G., Wyss, T., Fuertes Marraco, S. A., Scarpellino, L., Charmoy, M., Maas, R., Siddiqui, I., Tang, L., Joyce, J. A., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.09.005 · Cited by 218
Wang, D., Diao, H., Getzler, A. J., Rogal, W., Frederick, M. A., Milner, J., Yu, B., Crotty, S., Goldrath, A. W., & Pipkin, M. E. (2018) · Immunity · doi:10.1016/j.immuni.2018.03.028 · Cited by 201
Role of the Orphan Nuclear Receptor NR4A Family in T-Cell Biology
Odagiu, L., May, J., Boulet, S., Baldwin, T. A., & Labrecque, N. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2020.624122 · Cited by 110
Jennings, E., Elliot, T. A. E., Thawait, N., Kanabar, S., Yam-Puc, J. C., Ono, M., Toellner, K.-M., Wraith, D. C., Anderson, G., & Bending, D. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108328 · Cited by 94
Goronzy, J. J., Hu, B., Kim, C., Jadhav, R. R., & Weyand, C. M. (2018) · Journal of Leukocyte Biology · doi:10.1002/jlb.1ri0418-160r · Cited by 60
Therapeutic Cancer Vaccines—T Cell Responses and Epigenetic Modulation
Kartikasari, A. E. R., Prakash, M. D., Cox, M., Wilson, K., Boer, J. C., Cauchi, J. A., & Plebanski, M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2018.03109 · Cited by 54
E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation
Schauder, D. M., Shen, J., Chen, Y., Kasmani, M. Y., Kudek, M. R., Burns, R., & Cui, W. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013452118 · Cited by 40
Gamble, N., Bradu, A., Caldwell, J. A., McKeever, J., Bolonduro, O., Ermis, E., Kaiser, C., Kim, Y., Parks, B., Klemm, S., et al. (2024) · Nature Immunology · doi:10.1038/s41590-024-01807-y · Cited by 26
Yu, W., Zhao, X., Jalloh, A. S., Li, Y., Zhao, Y., Dinner, B., Yang, Y., Ouyang, S., Tian, T., Zhao, Z., et al. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c02602 · Cited by 21
Weber, E. W., Lynn, R. C., Parker, K. R., Anbunathan, H., Lattin, J., Sotillo, E., Good, Z., Malipatlolla, M., Xu, P., Vandris, P., et al. (2020) · doi:10.1101/2020.01.26.920496 · Cited by 18
“…JUNB, NFATC2), which are known to promote T cell exhaustion (Kurachi et al., 2014; Lynn et al., 2019; Man et al., 2017; Martinez et al., 2015; Scott-Browne et al., 2016), were highly enriched in accessible regions of the Always ON epigenome, but rendered less accessible following rest…”
BackgroundSekiya, T., Kasahara, H., Takemura, R., Fujita, S., Kato, J., Doki, N., Katayama, Y., Ozawa, Y., Takada, S., Eto, T., et al. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.2100808 · Cited by 16
Metadata
- Authors
- Scott-Browne, J. P., López-Moyado, I. F., Trifari, S., Wong, V., Chavez, L., Rao, A., & Pereira, R. M.
- Venue
- Immunity
- Publisher
- Elsevier BV
- Published
- 2016-12
- Volume
- 45
- Issue
- 6
- Pages
- 1327-1340
- ISSN
- 1074-7613 (ISSN-L)
- OpenAlex
- W2560265676
- Cited by
- 313
- References
- 13
- FWCI
- 13.80
- Type
- journal article
- Language
- en
- Open access
- bronze
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