1. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

2. Cox, D. B. T., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).

3. Chew, W. L. et al. A multifunctional AAV–CRISPR–Cas9 and its host response. Nat. Methods 13, 868–874 (2016).

4. Chew, W. L. Immunity to CRISPR Cas9 and Cas12a therapeutics. Wiley Interdiscip. Rev. Syst. Biol. Med. 10, e1408 (2018).

5. Lehrman, S. Virus treatment questioned after gene therapy death. Nature 401, 517–518 (1999).

6. Nayak, S. & Herzog, R. W. Progress and prospects: immune responses to viral vectors. Gene Ther. 17, 295–304 (2010).

7. Carapetis, J. R., Steer, A. C., Mulholland, E. K. & Weber, M. The global burden of group A streptococcal diseases. Lancet. Infect. Dis. 5, 685–694 (2005).

8. Charlesworth, C. T. et al. Identification of pre-existing adaptive immunity to Cas9 proteins in humans. Preprint at https://www.biorxiv.org/content/early/2018/01/05/243345 (2018).

9. Kleinstiver, B. P. et al. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529, 490–495 (2016).

10. Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

11. Vakulskas, C. A. et al. A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells. Nat. Med 24, 1216–1224 (2018).

12. Shaikh, N., Leonard, E. & Martin, J. M. Prevalence of streptococcal pharyngitis and streptococcal carriage in children: a meta-analysis. Pediatrics 126, e557–e564 (2010).

13. Frentsch, M. et al. Direct access to CD4+ T cells specific for defined antigens according to CD154 expression. Nat. Med. 11, 1118–1124 (2005).

14. Wolfl, M. et al. Activation-induced expression of CD137 permits detection, isolation, and expansion of the full repertoire of CD8+ T cells responding to antigen without requiring knowledge of epitope specificities. Blood 110, 201–210 (2007).

15. Schmueck-Henneresse, M. et al. Peripheral blood-derived virus-specific memory stem T cells mature to functional effector memory subsets with self-renewal potency. J. Immunol. 194, 5559–5567 (2015).

16. Lathrop, S. K. et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 478, 250–254 (2011).

17. Bacher, P. et al. Regulatory T Cell specificity directs tolerance versus allergy against aeroantigens in humans. Cell 167, 1067–1078.e16 (2016).

18. Sakaguchi, S., Sakaguchi, N., Asano, M., Itoh, M. & Toda, M. Immunologic self-tolerance maintained by activated T cells expressing IL-2 receptor alpha-chains (CD25). Breakdown of a single mechanism of self-tolerance causes various autoimmune diseases. J. Immunol. 155, 1151–1164 (1995).

19. Hori, S., Nomura, T. & Sakaguchi, S. Control of regulatory T Cell development by the transcription factor Foxp3. Science 299, 1057–1061 (2003).

20. Wing, K. et al. CTLA-4 contrÿol over Foxp3+ regulatory T cell function. Science 322, 271–275 (2008).

21. Schoenbrunn, A. et al. A converse 4-1BB and CD40 ligand expression pattern delineates activated regulatory T cells (T reg ) and conventional T cells enabling direct isolation of alloantigen-reactive natural Foxp3+ T reg . J. Immunol. 189, 5985–5994 (2012).

22. Polansky, J. K. et al. DNA methylation controls Foxp3 gene expression. Eur. J. Immunol. 38, 1654–1663 (2008).

23. Bacher, P. et al. Antigen-specific expansion of human regulatory T cells as a major tolerance mechanism against mucosal fungi. Mucosal Immunol. 7, 916–928 (2014).

24. Shmakov, S. et al. Diversity and evolution of class 2 CRISPR–Cas systems. Nat. Rev. Microbiol. 15, 169–182 (2017).

25. Harrison, O. J. & Powrie, F. M. Regulatory T cells and immune tolerance in the intestine. Cold Spring Harb. Perspect. Biol. 5, a018341 (2013).

26. Wakelin, S. J. et al. “Dirty little secrets”: endotoxin contamination of recombinant proteins. Immunol. Lett. 106, 1–7 (2006).

27. Hamano, R., Huang, J., Yoshimura, T., Oppenheim, J. J. & Chen, X. TNF optimally activatives regulatory T cells by inducing TNF receptor superfamily members TNFR2, 4-1BB and OX40. Eur. J. Immunol. 41, 2010–2020 (2011).

28. Lei, H., Schmidt-Bleek, K., Dienelt, A., Reinke, P. & Volk, H.-D. Regulatory T cell-mediated anti-inflammatory effects promote successful tissue repair in both indirect and direct manners. Front. Pharmacol. 6, 184 (2015).

29. Chandran, S. et al. Polyclonal regulatory T Cell therapy for control of inflammation in kidney transplants. Am. J. Transplant. 17, 2945–2954 (2017).

30. Bennett, C. L. et al. The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3. Nat. Genet. 27, 20–21 (2001).

31. Guilherme, L., Kalil, J. & Cunningham, M. Molecular mimicry in the autoimmune pathogenesis of rheumatic heart disease. Autoimmunity 39, 31–39 (2006).

32. Simhadri, V. L. et al. Prevalence of pre-existing antibodies to CRISPR-associated nuclease Cas9 in the USA population. Mol. Ther. Methods Clin. Dev 10, 105–112 (2018).

33. Arruda, V. R., Favaro, P. & Finn, J. D. Strategies to modulate immune responses: a new frontier for gene therapy. Mol. Ther. 17, 1492–1503 (2009).

34. Robins, H. S. et al. Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells. Blood 114, 4099–4107 (2009).

35. Sherwood, A. M. et al. Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. Sci. Transl. Med. 3, 90ra61 (2011).

36. Yousfi Monod, M. Y., Giudicelli, V., Chaume, D. & Lefranc, M.-P. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, i379–i385 (2004).

37. Johnson, D. R., Kurlan, R., Leckman, J. & Kaplan, E. L. The human immune response to streptococcal extracellular antigens: clinical, diagnostic, and potential pathogenetic implications. Clin. Infect. Dis. 50, 481–490 (2010).

38. Sen, E. S. & Ramanan, A. V. How to use antistreptolysin O titre. Arch. Dis. Child. Educ. Pract. Ed. 99, 231–238 (2014).

39. Heslop, H. E. et al. Long-term restoration of immunity against Epstein–Barr virus infection by adoptive transfer of gene-modified virus-specific T lymphocytes. Nat. Med. 2, 551–555 (1996).

40. Moosmann, A. et al. B cells immortalized by a mini-Epstein–Barr virus encoding a foreign antigen efficiently reactivate specific cytotoxic T cells. Blood 100, 1755–1764 (2002).

41. Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).

42. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

43. Johnson, M. et al. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5–W9 (2008).