Immunology and Cell Biology (2013) 91, 389–392 & 2013 Australasian Society for Immunology Inc. All rights reserved 0818-9641/13 www.nature.com/icb
NEWS AND COMMENTARIES Insights into T-cell differentiation
Inside out: decoding the transcriptome of effector and memory T cells Claudia Dominguez1 and Weiguo Cui2 Immunology and Cell Biology (2013) 91, 389–390; doi:10.1038/icb.2013.18; published online 30 April 2013
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ollowing an acute viral or intracellular bacterial infection, pathogen-specific CD8 T cells differentiate into various types of effector and memory CD8 T cells that help to mediate immediate pathogen clearance and provide long-term protective immunity.1 Although much effort and endeavor has been devoted to elucidating the mechanisms that regulate effector and memory CD8 T-cell activation, differentiation and survival, a fundamental understanding of the genetic pathways controlling these processes remains incomplete. In the issue of Nature Immunology, Best et al.2 take a systems biology approach to further characterize the global transcriptional programs that regulate effector and memory CD8 T-cell differentiation with unprecedented breadth, and bring new insights to the field. In this report, Best et al.2 use Listeria monocytogenes as a primary model pathogen and analyze the transcriptome of Listeriaspecific OT-I cells throughout the course of infection. The 7195 most differentially expressed genes over a broad time course of the CD8 T-cell response were selected as the core signature genes regulating CD8 T-cell differentiation. These core signature genes were then further parsed into 10 unbiased clusters according to the kinetics of their expression. These clusters can be largely divided into three groups, roughly defined by genes involved in T-cell activation and proliferation, genes promoting memory T-cell differentiation and genes regulating short-lived effector and effector memory T-cell differentiation. The first group consisted of the most acutely induced gene C Dominguez is at the Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA and W Cui is at the Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA E-mail:
[email protected]
clusters; genes involved in the initial cytokine and effector response (cluster I), preparation for cell division (cluster II) and cell cycle progression (cluster III). The expression of these gene clusters peaked between 12 and 48 h after activation and abruptly went down thereafter. The second group of gene clusters were transiently downregulated during the effector stage, but re-expressed at various levels in the memory stage. Clusters IV (naive and late memory), V (early effector and late memory), VII (memory precursor) and VIII (naive, late effector or memory) were included in this group. The third group of gene clusters included the genes whose expression was increased after activation, and then either sustained (cluster VI—short-term effector and memory and cluster X—late effector or memory) or gradually decreased (cluster IX—short-term effector or memory) in the memory phase (Figure 1). With these core gene clusters in hand, the authors went on to ask how the expression of these gene clusters correlates with memory T-cell formation as well as the metabolic and differentiation states of effector and memory CD8 T cells. First, they asked whether memory CD8 T cells had a unique transcriptional signature. Within each cluster, transcripts that were not expressed until day 45 or day 100 after infection were used to define memory and late memory signatures. Very few genes, 6 and 7 respectively, were identified as ‘memory specific’ and ‘late memory specific’. Strikingly, among this handful of genes, most have not been previously linked to memory T-cell formation or survival except bcl2. In depth, characterization of these genes may provide further insight into the mechanisms that memory CD8 T cells employ for their long-term survival and proliferative potential.
Next, the authors quantified the expression of genes encoding molecules that regulate metabolic pathways among these 10 gene clusters. They found that genes involved in glycolysis and fatty-acid biosynthesis were expressed within those gene clusters (II and III) found in rapidly dividing cells, whereas genes encoding molecules involved in fattyacid oxidation were expressed within gene clusters (V and VIII) found in resting naive or memory T cells. Together, these data provide the genetic evidence that a metabolic switch is indeed required for proper effector and memory T-cell differentiation.3,4 To better examine the regulation of differentiation of effector CD8 T cells, Best et al.2 used these core gene clusters to examine changes in gene expression in two major effector subsets—IL-7RloKLRG1hi short-lived effector cells and IL-7RhiKLRG1lo memory precursor effector cells. Given that the transcriptional regulators Id2 and Id3 have been shown to sustain KLRG1hi short-lived effector T-cell survival and promote KLRG1lo memory precursor cell potential respectively, Id2-WT and Id2-KO, Id3hi and Id3lo effector CD8 T-cell gene expression profiles were also included for comparison. This analysis revealed that genes in clusters III, VI, IX and X were preferentially expressed in the short-lived effector (KLRG1hi Id2-WT Id3lo) population, whereas clusters IV, V and VII were preferentially expressed in the memory precursor effector (KLRG1lo Id2-KO Id3hi) population. This observation was further confirmed using a published data set describing the signature genes of both IL-7Rlo shortlived effector cells and IL-7Rhi memory precursor effector cells during lymphocytic choriomeningitis virus (LCMV) infection.5 Together, this suggests that the kinetic patterns of core gene expression in effector and memory CD8 T cells are quite different,
News and Commentaries 390 Group I Activation and proliferation Clusters I, II, III Group II Naive and Memory Clusters IV, V, VII, VIII Group III Effector Differentiation Clusters VI, X, IX
Naive
Early Effector
Effector/Late Effector
Early Memory
Late Memory
Figure 1 Transcriptional nodes correlate with stages of CD8 T-cell differentiation. Expression profiling revealed a core set of 7195 genes with differential expression patterns during the course of Listeriaspecific CD8 T-cell differentiation from naive to late memory time points. Unbiased clustering of these core genes by the kinetics of their expression produced 10 clusters, which can be largely divided into three groups. Group I included early effector genes, genes downstream of TCR signaling, and genes important for cell growth and proliferation. Group II included genes expressed in naive T cells, which were downregulated after T-cell activation on a population level and re-expressed as CD8 T cells matured into memory. Group III genes were most highly expressed in effector and effector memory CD8 T cells, and slowly decreased after the effector stage.
and some core gene clusters can be used to identify memory T-cell potential (Figure 1). These data pose an intriguing question— could one use this data set to predict unknown regulators that control core gene cluster expression and ultimately affect effector and memory CD8 T-cell differentiation? Utilizing established co-regulated gene modules from the Immunological Genome (ImmGen) Project, the authors were able to not only identify many known transcriptional regulators of T-cell differentiation, but also predict many previously unappreciated regulators that likely modulate effector and memory T-cell differentiation. For example, Rora and Zeb2 were expressed preferentially in KLRG1hi cells, and their co-regulated gene
modules were also enriched within these cells. This suggests that ROR-a and Zeb2 may control the gene expression patterns of short-lived effector T cells. Besides these major findings, Best et al.2 also provided some additional insights. First, the core transcriptional signatures they identified are largely shared between polyclonal (endogenous) and monoclonal TCR transgenic CD8 T cells, suggesting that TCR transgenic cells still represent a valid model to analyze memory T-cell differentiation. Second, although the differences in cytokine milieu between different types of infection can potentially influence effector and memory CD8 T-cell differentiation,6,7 this study nicely shows that the core gene
expression among 10 clusters was conserved in effector and memory CD8 T cells in the context of a viral infection versus a bacterial infection. This suggests that differences in cytokine milieu do not drastically change the molecular signature of memory differentiation. Finally, one of the highlights from this systems biology analysis is that memory CD8 T cells were found to share some gene signatures with NKT and gd T cells, suggesting memory CD8 T cells may have gained some innate-like ability to mediate antigen-independent antimicrobial defense.8
1 Kaech SM, Cui W. Transcriptional control of effector and memory CD8 þ T cell differentiation. Nat Rev Immunol 2012; 12: 749–761. 2 Best JA, Blair DA, Knell J, Yang E, Mayya V, Doedens A et al. Transcriptional insights into the CD8 þ T cell response to infection and memory T cell formation. Nat Immunol 2013; 14: 404–412. 3 Pearce EL, Walsh MC, Cejas PJ, Harms GM, Shen H, Wang LS et al. Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature 2009; 460: 103–107. 4 Araki K, Turner AP, Shaffer VO, Gangappa S, Keller SA, Bachmann MF et al. mTOR regulates memory CD8 T-cell differentiation. Nature 2009; 460: 108–112. 5 Joshi NS, Cui W, Chandele A, Lee HK, Urso DR, Hagman J et al. Inflammation directs memory precursor and short-lived effector CD8( þ ) T cell fates via the graded expression of T-bet transcription factor. Immunity 2007; 27: 281–295. 6 Obar JJ, Jellison ER, Sheridan BS, Blair DA, Pham Q-M, Zickovich JM et al. Pathogen-induced inflammatory environment controls effector and memory CD8 þ T cell differentiation. J Immunol 2011; 187: 4967–4978. 7 Haring JS, Badovinac VP, Harty JT. Inflaming the CD8 þ T cell response. Immunity 2006; 25: 19–29. 8 Soudja SM, Ruiz AL, Marie JC, Lauvau G. Inflammatory monocytes activate memory CD8( þ ) T and innate NK lymphocytes independent of cognate antigen during microbial pathogen invasion. Immunity 2012; 37: 549–562.
Cell cycle control of T cell memory
Group 2 innate lymphoid cells show up in the skin Hergen Spits Immunology and Cell Biology (2013) 91, 390–392; doi:10.1038/icb.2013.24; published online 4 June 2013
Dr H Spits is at Academic Medical Center, Tytgat Institute for Liver and Intestinal Research, Amsterdam, The Netherlands E-mail:
[email protected]
Immunology and Cell Biology
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roup 2 innate lymphoid cells (ILCs) are effector cells shown to function in immunity against helminthic parasites and in tissue repair in lung and intestine. A recent
study that appeared in Nature Immunology characterized ILC2 in the skin.1 Dermal ILC2 strongly interact with mast cells and exhibit both pro- and anti-inflammatory activities.
