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Autophagy is essential for effector CD8(+) T cell survival and memory formation.

Xu X, Araki K, Li S, Han JH, Ye L, Tan WG, Konieczny BT, Bruinsma MW, Martinez J, Pearce EL, Green DR, Jones DP, Virgin HW, Ahmed R - Nat. Immunol. (2014)

Bottom Line: In contrast to the current paradigm, autophagy decreased in activated proliferating effector CD8(+) T cells and was then upregulated when the cells stopped dividing just before the contraction phase.Consistent with those findings, deletion of the gene encoding either of the autophagy-related molecules Atg5 or Atg7 had little to no effect on the proliferation and function of effector cells, but these autophagy-deficient effector cells had survival defects that resulted in compromised formation of memory T cells.Our studies define when autophagy is needed during effector and memory differentiation and warrant reexamination of the relationship between T cell activation and autophagy.

View Article: PubMed Central - PubMed

Affiliation: Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.

ABSTRACT
The importance of autophagy in the generation of memory CD8(+) T cells in vivo is not well defined. We report here that autophagy was dynamically regulated in virus-specific CD8(+) T cells during acute infection of mice with lymphocytic choriomeningitis virus. In contrast to the current paradigm, autophagy decreased in activated proliferating effector CD8(+) T cells and was then upregulated when the cells stopped dividing just before the contraction phase. Consistent with those findings, deletion of the gene encoding either of the autophagy-related molecules Atg5 or Atg7 had little to no effect on the proliferation and function of effector cells, but these autophagy-deficient effector cells had survival defects that resulted in compromised formation of memory T cells. Our studies define when autophagy is needed during effector and memory differentiation and warrant reexamination of the relationship between T cell activation and autophagy.

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Metabolomic and transcriptomic analysis of Atg7-dificient CD8 T cells. Atg7fl/flGzmb-Cre (KO) and control (Atg7fl/fl, WT) mice were infected with LCMV Armstrong. DbGP33+ CD8 T cells were isolated from mice 8 day p.i for analysis. (a) Pathways differentially regulated in Day 8 Atg7-deficient antigen-specific cells. Each column represents an independent experiment of samples pooled from 3 WT or KO mice; each row a pathway colored to indicate its p-value. (b) Gene set enrichment analysis (GSEA) of genes represented in T cells, which are associated with the metabolic enzymes underlying the most differentially regulated metabolic pathways (a) in KO vs. WT. p=0.024.
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Figure 7: Metabolomic and transcriptomic analysis of Atg7-dificient CD8 T cells. Atg7fl/flGzmb-Cre (KO) and control (Atg7fl/fl, WT) mice were infected with LCMV Armstrong. DbGP33+ CD8 T cells were isolated from mice 8 day p.i for analysis. (a) Pathways differentially regulated in Day 8 Atg7-deficient antigen-specific cells. Each column represents an independent experiment of samples pooled from 3 WT or KO mice; each row a pathway colored to indicate its p-value. (b) Gene set enrichment analysis (GSEA) of genes represented in T cells, which are associated with the metabolic enzymes underlying the most differentially regulated metabolic pathways (a) in KO vs. WT. p=0.024.

Mentions: To investigate the potential mechanism underlying the survival defects in the Atg7-deficient CD8 T cells, we performed metabolomic and transcriptomic analyses on antigen-specific T cells from Atg7-deficient (Atg7fl/flGzmb-Cre) or WT (Atg7fl/fl) mice 8 days following LCMV Armstrong infection. This time point was selected as representative of a transition time point in T cell differentiation before significant loss of Atg7-deficient cells has occurred. In the DbGP33+ CD8 T cells isolated from mice 8 day p.i, the overall gene expression pattern of the Atg7-deficient CD8 T cells closely resembled that of the WT group; only a small number of genes showed significantly different expression between the two groups in the DNA microarray data, mostly associated with cell cycle (data not shown). However, these cells exhibited distinct metabolic profiles measured on a liquid chromatography coupled mass spectrometry (LC-MS) metabolomics platform. Among the metabolites that were significantly different between Atg7-sufficent and deficient cells (Supplementary Table 1), many are contained within well-defined metabolic pathways with clear links to cell survival, as well as some of which have been implicated in T cell differentiation (Supplementary Fig. 6). For example, among the pathways that were significantly different between genotypes are the carnitine shuttle and di-unsaturated fatty acid beta-oxidation, both of which are part of fatty acid metabolism in the mitochondria (Fig. 7a). T cell-intrinsic mitochondrial fatty acid oxidation has been shown to be a critical metabolic pathway for the stable development of long-lived memory T cells 16, 17. These data could indicate that autophagy contributes to the production of the lipid substrates for mitochondrial fatty acid oxidation and the fueling of oxidative phosphorylation (OXPHOS) in these cells 28. Consistent with a role for autophagy in lipid metabolism in T cells during the transition to the memory phase, our metabolite analysis showed that lipid biosynthetic pathways were dysregulated in the absence of Atg7 (Fig. 7a). Also of note, glucosamine 6 phosphate and glycan biosynthesis pathways were perturbed in Atg7-deficient T cells (Fig. 7a and Supplementary Fig. 6). The hexosamine pathway provides substrates for the glycosylation of growth factor cytokine receptors, leading to receptor stability and the maintenance of survival signals 29. Given the importance of growth factor cytokines in supporting the development of memory T cells 2, it is possible that T cells lacking autophagy machinery cannot maintain the proper growth factor signals that support memory T cell development, linking autophagy to glycosylation and the maintenance of cellular metabolism. Importantly, these metabolomics data were further validated by examining the levels of gene expression of the enzymes associated these metabolite activities. Using Gene set enrichment analysis30 and these enzymes as a gene set, the gene expression for these metabolic activities was clearly associated with the Atg7 deficient genotype (Fig. 7b and Supplementary Table 2). Overall, several metabolic pathways were altered in Atg7-deficient T cells day 8 pi, and when integrated with our transcriptomic studies suggest that autophagy supports metabolic homeostasis in CD8 T cells during the transition to memory phase.


Autophagy is essential for effector CD8(+) T cell survival and memory formation.

Xu X, Araki K, Li S, Han JH, Ye L, Tan WG, Konieczny BT, Bruinsma MW, Martinez J, Pearce EL, Green DR, Jones DP, Virgin HW, Ahmed R - Nat. Immunol. (2014)

Metabolomic and transcriptomic analysis of Atg7-dificient CD8 T cells. Atg7fl/flGzmb-Cre (KO) and control (Atg7fl/fl, WT) mice were infected with LCMV Armstrong. DbGP33+ CD8 T cells were isolated from mice 8 day p.i for analysis. (a) Pathways differentially regulated in Day 8 Atg7-deficient antigen-specific cells. Each column represents an independent experiment of samples pooled from 3 WT or KO mice; each row a pathway colored to indicate its p-value. (b) Gene set enrichment analysis (GSEA) of genes represented in T cells, which are associated with the metabolic enzymes underlying the most differentially regulated metabolic pathways (a) in KO vs. WT. p=0.024.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4232981&req=5

Figure 7: Metabolomic and transcriptomic analysis of Atg7-dificient CD8 T cells. Atg7fl/flGzmb-Cre (KO) and control (Atg7fl/fl, WT) mice were infected with LCMV Armstrong. DbGP33+ CD8 T cells were isolated from mice 8 day p.i for analysis. (a) Pathways differentially regulated in Day 8 Atg7-deficient antigen-specific cells. Each column represents an independent experiment of samples pooled from 3 WT or KO mice; each row a pathway colored to indicate its p-value. (b) Gene set enrichment analysis (GSEA) of genes represented in T cells, which are associated with the metabolic enzymes underlying the most differentially regulated metabolic pathways (a) in KO vs. WT. p=0.024.
Mentions: To investigate the potential mechanism underlying the survival defects in the Atg7-deficient CD8 T cells, we performed metabolomic and transcriptomic analyses on antigen-specific T cells from Atg7-deficient (Atg7fl/flGzmb-Cre) or WT (Atg7fl/fl) mice 8 days following LCMV Armstrong infection. This time point was selected as representative of a transition time point in T cell differentiation before significant loss of Atg7-deficient cells has occurred. In the DbGP33+ CD8 T cells isolated from mice 8 day p.i, the overall gene expression pattern of the Atg7-deficient CD8 T cells closely resembled that of the WT group; only a small number of genes showed significantly different expression between the two groups in the DNA microarray data, mostly associated with cell cycle (data not shown). However, these cells exhibited distinct metabolic profiles measured on a liquid chromatography coupled mass spectrometry (LC-MS) metabolomics platform. Among the metabolites that were significantly different between Atg7-sufficent and deficient cells (Supplementary Table 1), many are contained within well-defined metabolic pathways with clear links to cell survival, as well as some of which have been implicated in T cell differentiation (Supplementary Fig. 6). For example, among the pathways that were significantly different between genotypes are the carnitine shuttle and di-unsaturated fatty acid beta-oxidation, both of which are part of fatty acid metabolism in the mitochondria (Fig. 7a). T cell-intrinsic mitochondrial fatty acid oxidation has been shown to be a critical metabolic pathway for the stable development of long-lived memory T cells 16, 17. These data could indicate that autophagy contributes to the production of the lipid substrates for mitochondrial fatty acid oxidation and the fueling of oxidative phosphorylation (OXPHOS) in these cells 28. Consistent with a role for autophagy in lipid metabolism in T cells during the transition to the memory phase, our metabolite analysis showed that lipid biosynthetic pathways were dysregulated in the absence of Atg7 (Fig. 7a). Also of note, glucosamine 6 phosphate and glycan biosynthesis pathways were perturbed in Atg7-deficient T cells (Fig. 7a and Supplementary Fig. 6). The hexosamine pathway provides substrates for the glycosylation of growth factor cytokine receptors, leading to receptor stability and the maintenance of survival signals 29. Given the importance of growth factor cytokines in supporting the development of memory T cells 2, it is possible that T cells lacking autophagy machinery cannot maintain the proper growth factor signals that support memory T cell development, linking autophagy to glycosylation and the maintenance of cellular metabolism. Importantly, these metabolomics data were further validated by examining the levels of gene expression of the enzymes associated these metabolite activities. Using Gene set enrichment analysis30 and these enzymes as a gene set, the gene expression for these metabolic activities was clearly associated with the Atg7 deficient genotype (Fig. 7b and Supplementary Table 2). Overall, several metabolic pathways were altered in Atg7-deficient T cells day 8 pi, and when integrated with our transcriptomic studies suggest that autophagy supports metabolic homeostasis in CD8 T cells during the transition to memory phase.

Bottom Line: In contrast to the current paradigm, autophagy decreased in activated proliferating effector CD8(+) T cells and was then upregulated when the cells stopped dividing just before the contraction phase.Consistent with those findings, deletion of the gene encoding either of the autophagy-related molecules Atg5 or Atg7 had little to no effect on the proliferation and function of effector cells, but these autophagy-deficient effector cells had survival defects that resulted in compromised formation of memory T cells.Our studies define when autophagy is needed during effector and memory differentiation and warrant reexamination of the relationship between T cell activation and autophagy.

View Article: PubMed Central - PubMed

Affiliation: Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.

ABSTRACT
The importance of autophagy in the generation of memory CD8(+) T cells in vivo is not well defined. We report here that autophagy was dynamically regulated in virus-specific CD8(+) T cells during acute infection of mice with lymphocytic choriomeningitis virus. In contrast to the current paradigm, autophagy decreased in activated proliferating effector CD8(+) T cells and was then upregulated when the cells stopped dividing just before the contraction phase. Consistent with those findings, deletion of the gene encoding either of the autophagy-related molecules Atg5 or Atg7 had little to no effect on the proliferation and function of effector cells, but these autophagy-deficient effector cells had survival defects that resulted in compromised formation of memory T cells. Our studies define when autophagy is needed during effector and memory differentiation and warrant reexamination of the relationship between T cell activation and autophagy.

Show MeSH
Related in: MedlinePlus