Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).
Zhao, T., Zhang, Z. N., Rong, Z. & Xu, Y. Immunogenicity of induced pluripotent stem cells. Nature 474, 212–215 (2011).
Boyd, A. S. & Wood, K. J. Characteristics of the early immune response following transplantation of mouse ES cell derived insulin-producing cell clusters. PLoS ONE 5, e10965 (2010).
Nicholls, S. et al. Secondary anchor polymorphism in the HA-1 minor histocompatibility antigen critically affects MHC stability and TCR recognition. Proc. Natl Acad. Sci. USA 106, 3889–3894 (2009).
Mullally, A. & Ritz, J. Beyond HLA: the significance of genomic variation for allogeneic hematopoietic stem cell transplantation. Blood 109, 1355–1362 (2007).
Ben-David, U., Nudel, N. & Benvenisty, N. Immunologic and chemical targeting of the tight-junction protein Claudin-6 eliminates tumorigenic human pluripotent stem cells. Nat. Commun. 4, 1992 (2013).
Jia, F. et al. A nonviral minicircle vector for deriving human iPS cells. Nat. Methods 7, 197–199 (2010).
Meissner, A., Wernig, M. & Jaenisch, R. Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. Nat. Biotechnol. 25, 1177–1181 (2007).
Li, Z. et al. Differentiation, survival, and function of embryonic stem cell derived endothelial cells for ischemic heart disease. Circulation 116, 146–154 (2007).
Han, Y. M., Guo, Q. L., Zhang, M. G., Chen, Z. B. & Cao, X. T. CD69(+)CD4(+)CD25(-) T cells, a new subset of regulatory T cells, suppress T cell proliferation through membrane-bound TGF-beta 1. J. Immunol. 182, 111–120 (2009).
Wang, T. et al. Regulation of the innate and adaptive immune responses by Stat-3 signaling in tumor cells. Nat. Med. 10, 48–54 (2004).
Welte, T. et al. STAT3 deletion during hematopoiesis causes Crohn's disease-like pathogenesis and lethality: a critical role of STAT3 in innate immunity. Proc. Natl Acad. Sci. USA 100, 1879–1884 (2003).
Kortylewski, M. et al. Inhibiting STAT3 signaling in the hematopoietic system elicits multicomponent antitumor immunity. Nat. Med. 11, 1314–1321 (2005).
Peppa, D. et al. Up-regulation of a death receptor renders antiviral T cells susceptible to NK cell-mediated deletion. J. Exp. Med. 210, 99–114 (2013).
Zhang, Y., Feng, X. H. & Derynck, R. Smad3 and Smad4 cooperate with c-Jun/c-Fos to mediate TGF-beta-induced transcription. Nature 394, 909–913 (1998).
Rubtsov, Y. P. et al. Regulatory T cell-derived interleukin-10 limits inflammation at environmental interfaces. Immunity 28, 546–558 (2008).
Le Texier, L. et al. Immunoregulatory function of IL-27 and TGF-beta1 in cardiac allograft transplantation. Transplantation 94, 226–233 (2012).
Schietinger, A., Delrow, J. J., Basom, R. S., Blattman, J. N. & Greenberg, P. D. Rescued tolerant CD8 T cells are preprogrammed to reestablish the tolerant state. Science 335, 723–727 (2012).
Narsinh, K. H. et al. Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J. Clin. Invest. 121, 1217–1221 (2011).
Deaglio, S. et al. Adenosine generation catalyzed by CD39 and CD73 expressed on regulatory T cells mediates immune suppression. J. Exp. Med. 204, 1257–1265 (2007).
Perez, V. L. et al. Induction of peripheral T cell tolerance in vivo requires CTLA-4 engagement. Immunity 6, 411–417 (1997).
Keir, M. E., Butte, M. J., Freeman, G. J. & Sharpe, A. H. PD-1 and its ligands in tolerance and immunity. Annu. Rev. Immunol. 26, 677–704 (2008).
Nurieva, R. I. et al. The E3 ubiquitin ligase GRAIL regulates T cell tolerance and regulatory T cell function by mediating T cell receptor-CD3 degradation. Immunity 32, 670–680 (2010).
Shembade, N. et al. The E3 ligase Itch negatively regulates inflammatory signaling pathways by controlling the function of the ubiquitin-editing enzyme A20. Nat. Immunol. 9, 254–262 (2008).
Zilberberg, J., McElhaugh, D., Gichuru, L. N., Korngold, R. & Friedman, T. M. Inter-strain tissue-infiltrating T cell responses to minor histocompatibility antigens involved in graft-versus-host disease as determined by Vbeta spectratype analysis. J. Immunol. 180, 5352–5359 (2008).
Gagne, K. et al. Highly altered V beta repertoire of T cells infiltrating long-term rejected kidney allografts. J. Immunol. 164, 1553–1563 (2000).
Guillet, M. et al. Different qualitative and quantitative regulation of V beta TCR transcripts during early acute allograft rejection and tolerance induction. J. Immunol. 168, 5088–5095 (2002).
Dietrich, P. Y. et al. Analysis of T-cell receptor variability in transplanted patients with acute graft-versus-host disease. Blood 80, 2419–2424 (1992).
Matsutani, T. et al. Restricted usage of T-cell receptor alpha-chain variable region (TCRAV) and T-cell receptor beta-chain variable region (TCRBV) repertoires after human allogeneic haematopoietic transplantation. Br. J. Haematol. 109, 759–769 (2000).
Bhattacharya, A. On a measure of divergence between two statistical populations defined by their probability distribution. Sankhyā Indian J. Statist. 7, 401–406 (1943).
Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010).
Bar-Nur, O., Russ, H. A., Efrat, S. & Benvenisty, N. Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell 9, 17–23 (2011).
Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73 (2011).
Cunningham, J. J., Ulbright, T. M., Pera, M. F. & Looijenga, L. H. Lessons from human teratomas to guide development of safe stem cell therapies. Nat. Biotechnol. 30, 849–857 (2012).
Araki, R. et al. Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells. Nature 494, 100–104 (2013).
Guha, P., Morgan, J. W., Mostoslavsky, G., Rodrigues, N. P. & Boyd, A. S. Lack of immune response to differentiated cells derived from syngeneic induced pluripotent stem cells. Cell Stem Cell 12, 407–412 (2013).
Sun, B., Chen, M., Hawks, C. L., Pereira-Smith, O. M. & Hornsby, P. J. The minimal set of genetic alterations required for conversion of primary human fibroblasts to cancer cells in the subrenal capsule assay. Neoplasia 7, 585–593 (2005).
Woo, E. Y. et al. Regulatory CD4(+)CD25(+) T cells in tumors from patients with early-stage non-small cell lung cancer and late-stage ovarian cancer. Cancer Res. 61, 4766–4772 (2001).
Blank, C. et al. PD-L1/B7H-1 inhibits the effector phase of tumor rejection by T cell receptor (TCR) transgenic CD8+ T cells. Cancer Res. 64, 1140–1145 (2004).
Baitsch, L. et al. Exhaustion of tumor-specific CD8(+) T cells in metastases from melanoma patients. J. Clin. Invest. 121, 2350–2360 (2011).
Walker, L. S. K. & Abbas, A. K. The enemy within: Keeping self-reactive T cells at bay in the periphery. Nat. Rev. Immunol. 2, 11–19 (2002).
Kohyama, M. et al. Inducible costimulator-dependent IL-10 production by regulatory T cells specific for self-antigen. Proc. Natl Acad. Sci. USA 101, 4192–4197 (2004).
Akkaraju, S. et al. A range of CD4 T cell tolerance: partial inactivation to organ-specific antigen allows nondestructive thyroiditis or insulitis. Immunity 7, 255–271 (1997).
Batsford, S. et al. Is monitoring of FOXP3 Treg cells in renal transplants during acute cellular rejection episodes useful? Clin. Nephrol. 75, 101–106 (2011).
Miyao, T. et al. Plasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells. Immunity 36, 262–275 (2012).
Carlson, C. S. et al. Using synthetic templates to design an unbiased multiplex PCR assay. Nat. Commun. 4, 2680 (2013).
Meyer, E. H. et al. A distinct evolution of the T-cell repertoire categorizes treatment refractory gastrointestinal acute graft-versus-host disease. Blood 121, 4955–4962 (2013).