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Moskowitz DM, Zhang DW, Hu B, Le Saux S, Yanes RE, Ye Z, Buenrostro JD, Weyand CM, Greenleaf WJ, Goronzy JJ. Epigenomics of human CD8 T cell differentiation and aging. Sci Immunol 2017; 2:eaag0192. [PMID: 28439570 PMCID: PMC5399889 DOI: 10.1126/sciimmunol.aag0192] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we inferred the transcription factor binding activities correlated with naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles implicated for BATF, ETS1, Eomes, and Sp1. Extending our analysis to aged humans, we found that the differences between the memory and naive subsets were largely preserved across age, but that naive and central memory cells from older individuals exhibited a shift toward more differentiated patterns of chromatin openness. Additionally, aged naive cells displayed a loss in chromatin accessibility at gene promoters, largely associated with a decrease in NRF1 binding. This shift was implicated in a marked drop-off in the ability of the aged naive cells to transcribe respiratory chain genes, which may explain the reduced capacity of oxidative phosphorylation in older naïve cells. Our findings identify BATF- and NRF1-driven gene regulation as potential targets for delaying CD8 T cell aging and restoring function.
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Affiliation(s)
- David M Moskowitz
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, California
| | - David W Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Bin Hu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Sabine Le Saux
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Rolando E Yanes
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Zhongde Ye
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University, School of Medicine, Stanford, California
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305; and Department of Medicine, Veterans Affairs Palo Alto Health Care, System, Palo Alto, CA 94306
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Vizcaíno C, Mansilla S, Portugal J. Sp1 transcription factor: A long-standing target in cancer chemotherapy. Pharmacol Ther 2015; 152:111-24. [PMID: 25960131 DOI: 10.1016/j.pharmthera.2015.05.008] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/04/2015] [Indexed: 11/25/2022]
Abstract
Sp1 (specificity protein 1) is a well-known member of a family of transcription factors that also includes Sp2, Sp3 and Sp4, which are implicated in an ample variety of essential biological processes and have been proven important in cell growth, differentiation, apoptosis and carcinogenesis. Sp1 activates the transcription of many cellular genes that contain putative CG-rich Sp-binding sites in their promoters. Sp1 and Sp3 proteins bind to similar, if not the same, DNA tracts and compete for binding, thus they can enhance or repress gene expression. Evidences exist that the Sp-family of proteins regulates the expression of genes that play pivotal roles in cell proliferation and metastasis of various tumors. In patients with a variety of cancers, high levels of Sp1 protein are considered a negative prognostic factor. A plethora of compounds can interfere with the trans-activating activities of Sp1 and other Sp proteins on gene expression. Several pathways are involved in the down-regulation of Sp proteins by compounds with different mechanisms of action, which include not only the direct interference with the binding of Sp proteins to their putative DNA binding sites, but also promoting the degradation of Sp protein factors. Down-regulation of Sp transcription factors and Sp1-regulated genes is drug-dependent and it is determined by the cell context. The acknowledgment that several of those compounds are safe enough might accelerate their introduction into clinical usage in patients with tumors that over-express Sp1.
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Affiliation(s)
- Carolina Vizcaíno
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain
| | - Sylvia Mansilla
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain
| | - José Portugal
- Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, E-08028 Barcelona, Spain.
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